ONONDAGA LAKE AMBIENT MONITORING PROGRAM

2009 ANNUAL REPORT

ONONDAGA COUNTY, NEW YORK

FINAL

NOVEMBER 2010

Prepared for:

ONONDAGA COUNTY DEPARTMENT OF WATER ENVIRONMENT PROTECTON

Syracuse, NY

Prepared by:

EcoLogic, LLC

Aquatic, Terrestrial and Wetland Consultants

Cazenovia, NY

Lars Rudstam, Ph.D.

Cornell Biological Field Station

Bridgeport, NY

Anchor QEA, LLC

Liverpool, NY

A MESSAGE FROM THE COUNTY EXECUTIVE

Onondaga Lake is on the road to recovery. This report of the 2009 Ambient Monitoring Program carried out by the Onondaga County Department of Water Environment Protection (DWEP) documents significant progress toward improving water quality and habitat conditions. I encourage all residents of Onondaga County to read this report and to take pride in the value of our investment in infrastructure improvements.

As in 2008, the 2009 AMP annual report is a concise summary of major findings with links to supporting information. This paperless format was developed to advance two objectives: first, to reach a broader audience, and second, to continue to find ways to reduce our environmental footprint, through our commitment to green initiatives. We are confident that this format will enable more of our County leaders and citizens to become better informed regarding the condition of Onondaga Lake and its watershed. Additional program information, including annual reports from previous years, can be found on the County web site www.ongov.net/wep

Joanne C. Mahoney

Onondaga County Executive

_____________________________________________________________________________________

A MESSAGE FROM THE COMMISSIONER OF WATER ENVIRONMENT PROTECTION

The Department of Water Environment Protection is responsible for collecting and treating wastewater from homes and businesses throughout the County. As Commissioner, I am proud to lead our dedicated staff under a name that reflects Onondaga County’s firm commitment to protecting the water resources we all share. The Department is required to complete an intensive survey of water quality conditions in the Onondaga Lake watershed each year. This publication is a summary of the findings of the 2009 Ambient Monitoring Program (AMP). 2009 marked the 40^th consecutive year that Onondaga County successfully completed a monitoring program of Onondaga Lake and adjacent waters. Results of this long-term monitoring effort are used to track how Onondaga Lake is responding to pollution abatement activities. Current conditions and trends in water quality and the lake’s biological community are highlighted in this document. Comments on this report are encouraged and may be directed to Jeanne C. Powers at 315-435-2260 or email JeannePowers@ongov.net

Patricia M. Pastella, P.E., BCEE

Commissioner

Key Features of this Report

This report presents the findings of Onondaga County’s Ambient Monitoring Program (AMP) for 2009. The County’s annual monitoring program is designed to evaluate compliance with water quality standards and trends as improvements to the wastewater collection and treatment infrastructure are completed. Each year, the Onondaga County Department of Water Environment Protection collects extensive water quality and biological data to characterize Onondaga Lake and its watershed. This summary report of 2009 conditions provides a synopsis of the extensive data to the many stakeholders interested in Onondaga Lake.

The 2009 report was prepared and distributed as an electronic document. Key results and supporting tables and graphics are included in the main document, with links to supporting tables, technical reports and graphics in an electronic library. The report and supporting files are available on CD and on the Onondaga County web site www.ongov.net. Throughout the document, the reader will find hyperlinks to more detailed tables, graphs and reports. Simple definitions of many of the technical terms are included (roll the computer mouse over a highlighted term). A folder icon at the end of each section (illustrated below) provides links to the section of the electronic library where additional materials are archived.

Once in the library of supporting documents, the reader can navigate back to the main report using web browser navigation tools. There are more than 500 supporting tables and graphics in the library of supporting materials. While each hyperlink has been checked, it is possible that some features may not be enabled on every computer’s operating system. Feedback on the functionality of the electronic features of the document is welcome, please contact JeannePowers@ongov.net with comments.

TABLE OF CONTENTS

Executive Summary

1. Introduction to the AMP

1.1 Regulatory requirements

1.2 Ambient Monitoring Program Design

1.3 Turning Data into Information: Metrics

1.4 Mathematical modeling

1.5 Timeline of Onondaga Lake and Watershed Events, 1998-2009

2. Onondaga Lake and its Watershed

3. Tributary Results: 2009 Water Quality Status and Trends

3.1 Climatic Conditions

3.2 Tributary Water Quality and Annual Loads

Compliance with Ambient Water Quality Standards

Compliance with Metro SPDES Permit

Flows and Loads

Storm Events

Wet and Dry Weather Events

Trends

4. Onondaga Lake: 2009 Water Quality Status and Trends

4.1 Trophic State Indicator Parameters

Total Phosphorus (TP)

Chlorophyll-a

Secchi Disk Transparency

Trophic State Index

4.2 Ammonia and Nitrite

4.3 Recreational Quality

4.4 Metro Improvements and Lake Response

4.5 Seneca River

5. Biology and Food Web: 2009 Results and Trends

5.1 Phytoplankton

5.2 Macrophytes

5.3 Zooplankton

5.4 Zebra and Quagga Mussels

5.5 Fish

Richness and Diversity

Reproductive Success

Recreational Fishery

Abnormalities

6. Integrated Assessment of the Food Web

7. Progress with Related Initiatives

8. Emerging Issues and Recommendations

9. Literature Cited

LINK TO LIBRARY FILES

LIST OF TABLES AND FIGURES BY SECTION

EXECUTIVE SUMMARY

Table EX-1 Summary of Metrics, Onondaga Lake 2009.

SECTION 1: Introduction to the AMP

Table 1-1. Summary of Current Fish Consumption Advisories for Onondaga Lake.

Table 1-2 Metro Compliance Schedule.

Table 1-3 CSO Compliance Schedule.

Table 1-4 Data Analysis and Interpretation Plan.

Table 1-5 Summary of metrics used to evaluate progress toward improvement.

Figure 1-1 Tributary and Lake Regulatory Classification and Subwatershed Boundaries.

Figure 1-2 Map of monitoring locations, Onondaga Lake and tributaries.

SECTION 2: Onondaga Lake and its Watershed

Table 2-1 Morphometric characteristics of Onondaga Lake.

Figure 2-1 Hydrologic input to Onondaga Lake, as percent of total.

Figure 2-2 Land Cover Classes, 2001, Onondaga Lake Watershed.

SECTION 3: Tributary Results: 2009 Results and Trends

Table 3-1 Percent of Onondaga Lake tributary sample results in compliance with NYS water quality standards, 2009.

Table 3-2 Flow-weighted average concentration of selected parameters, 2009, Onondaga Lake tributaries.

Table 3-3 Annual loading of selected water quality parameters to Onondaga Lake, 2009.

Table 3-4 Percent annual loading contribution by gauged inflow, 2009.

Table 3-5 Tributary and Metro Total Phosphorus (TP) Loading to Onondaga Lake, pre-ACJ and post-ActiFlo implementation.

Table 3-6 Tributary and Metro Soluble Reactive Phosphorus (SRP) Loading to Onondaga Lake, pre-ACJ and post-ActiFlo implementation.

Figure 3-1 Metro NH₃-N, monthly average discharge compared to permit limit.

Figure 3-2 Metro effluent compliance for total phosphorus concentration, 12-month rolling average.

Figure 3-3 Metro and Tributary Sources of TP to Onondaga Lake, 1998 to 2009.

Figure 3-4 Metro and Tributary Sources of SRP to Onondaga Lake, 1998 to 2009.

Figure 3-5 Total phosphorus external loading to Onondaga Lake (Water Year) compared with South Deep total phosphorus concentrations (summer) in upper waters.

Figure 3-6 Metro Loading of Ammonia, Nitrite, Nitrate and Organic Nitrogen, 1998‐2009.

Figure 3-7 Onondaga Lake Ammonia Sources, 1998 and 2009.

SECTION 4: Onondaga Lake: 2009 Status and Trends

Table 4-1 Percent of Ammonia Measurements in Compliance with Ambient Water Quality Standards, Onondaga Lake, 1998-2009.

Table 4-2 Nearshore Secchi disk transparency statistical summary for Onondaga Lake, 2009.

Figure 4-1 Onondaga Lake Summer Average Total P Concentration (0‐3m), 1998‐2009.

Figure 4-2 Onondaga Lake Summer Algal Bloom Frequency, 1998‐2009.

Figure 4-3 Onondaga Lake Chlorophyll‐a Concentration, 1998-2009.

Figure 4-4 TP and Chlorophyll-a concentrations, Onondaga Lake 2007-2009 compared with Oneida and Finger Lakes.

Figure 4-5 Onondaga Lake Secchi Disk Transparency, January‐December, 2009.

Figure 4-6 Carlson Trophic State Index (TSI) Onondaga Lake, 1998- 2009.

Figure 4-7 Onondaga Lake Fecal Coliform Bacteria Abundance, Summer Geometric Mean, 1999‐2009.

Figure 4-8 Onondaga Lake Fecal Coliform Bacteria Compliance, April – October 2009.

Figure 4-9 Relationship between TP Loading (all sources) and Onondaga Lake TP Concentration, 1990‐2009.

Figure 4-10 Nitrogen: Phosphorus Ratio, 1998‐2009.

Figure 4‐11 Onondaga Lake Minimum DO in upper waters (0-3m) during fall mixing period, 1998‐2009.

Figure 4-12 Comparison of soluble reactive phosphorus (SRP) and nitrate-N concentrations with dissolved oxygen concentrations in South Deep lower waters of Onondaga Lake during 2009.

Figure 4-13 Three Rivers System Study Area.

SECTION 5: Biology and Food Web: 2009 Results and Trends

Table 5-1 2009 Macrophyte Field Survey Results.

Table 5-2 List of Fish Species Identified in Onondaga Lake, 2009

Figure 5-1 Reduction in Onondaga Lake phytoplankton standing crop, 1998 - 2009.

Figure 5-2 2009 Proportional biomass of phytoplankton divisions in Onondaga Lake.

Figure 5-3 Onondaga Lake Phytoplankton Community Structure and Biomass, February-December 2009.

Figure 5-4 Onondaga Lake South Deep, comparison of diatoms and silica concentrations in 2009.

Figure 5-5 Average biomass of zooplankton, proportion of major groups across time.

Figure 5-6 Biomass of different Daphnia species in Onondaga Lake.

Figure 5-7 Time trends in average size of all crustaceans from 1999 to 2009 in Onondaga Lake.

Figure 5-8 Average crustacean zooplankton length (mm) in Onondaga Lake in 2009.

Figure 5-9 Onondaga Lake Dreissenid Mussel Average Density and Biomass with Standard Deviation, 2002-2009.

Figure 5-10 Onondaga Lake Relative Abundance of Dreissenid Mussels, 2002-2009.

Figure 5-11 Comparison of DELTFM for all fish evaluated with brown bullhead only.

SECTION 6: Integrated Assessment of the Food Web

Figure 6-1 Food web effects on water clarity

SECTION 7: Progress with Related Initiatives

No figures or tables

SECTION 8: Emerging Issues and Recommendations

No figures or tables

SECTION 9: Literature Cited

List of Acronyms

Executive Summary

The 2009 Annual Report of Onondaga County’s Ambient Monitoring Program (AMP) provides an overview of the results of the extensive monitoring effort underway to characterize Onondaga Lake and its watershed. Conducted annually since 1970, the AMP represents an unparalleled investment in long-term monitoring of a complex aquatic ecosystem.

In 1998, an Amended Consent Judgment (ACJ) between Onondaga County, New York State and Atlantic States Legal Foundation was signed to resolve a lawsuit filed against Onondaga County for violations of the Clean Water Act. The lawsuit alleged that discharges from the Metropolitan Syracuse Wastewater Treatment Plant (Metro) exceeded the facility’s permitted discharge limits, and that overflows from the combined sewer system (CSOs) were not in compliance with state and federal requirements. The ACJ obligates the County to undertake a phased program of wastewater collection and treatment improvements, monitor water quality response, and report annually on progress towards compliance. This annual report fulfills the requirement for monitoring and reporting. The ACJ has been amended four times since 1998 to reflect changes in regulations, technology and environmental conditions, most recently by stipulation in November 2009. Among other requirements, the November 2009 amendment extends the schedule of required infrastructure improvements and monitoring through the year 2018.

The AMP is designed to document the lake’s response to pollution control measures. Samples are collected throughout the entire watershed to identify sources of materials (nutrients, sediment, bacteria and chemicals) to the lake. An intensive in-lake monitoring program examines water quality conditions and the interactions between Onondaga Lake and the Seneca River. Data are evaluated for compliance with water quality standards and analyzed for trends. In addition to the water quality monitoring effort, the AMP examines the nature of the lake ecosystem by characterizing the species composition and abundance of fish, phytoplankton, zooplankton, benthic invertebrates, aquatic plants and dreissenid (zebra and quagga) mussels.

Excessive discharges of municipal and industrial wastewaters, structural modifications resulting in altered water levels, loss of wetlands, and runoff from urban and rural areas have degraded the quality of Onondaga Lake. Contact recreation has been precluded by elevated bacteria counts, algal blooms from excessive phosphorus and poor water clarity. Conditions for aquatic life were compromised by high ammonia and nitrite concentrations, low dissolved oxygen levels, and lack of habitat. Onondaga Lake’s degraded water quality resulted from multiple sources of pollution. Increasingly stringent regulations and major investments by the public and private sectors have reduced the pollutant inputs to Onondaga Lake, resulting in improved water quality and habitat conditions.

In light of the lake’s water quality conditions, the primary focus of the improvements to the wastewater treatment system has been to provide a higher level of treatment for ammonia and phosphorus at Metro. Two new treatment systems have been brought on line to reduce Metro’s discharge of ammonia and phosphorus to Onondaga Lake. The Biological Aerated Filter (BAF) system has resulted in year-round nitrification (conversion of ammonia to nitrate) of the wastewater. This innovative technology, which became fully operational in 2004, has resulted in a 98% decrease in Metro’s ammonia loading to the lake. Phosphorus removal is achieved using a physical-chemical High-Rate Flocculated Settling (HRFS) technology, known as Actiflo. The system came on line in 2005 to meet an interim effluent limit of 0.12 mg/L of total phosphorus. This technology has resulted in an 86% decrease in Metro’s total phosphorus loading to the lake. As part of the November 2009, fourth stipulation to the ACJ, the total phosphorus discharge limit from Metro will be revised downward to 0.10 mg/L, effective in November, 2010. In addition to these improvements focused on ammonia and phosphorus, the technology employed for disinfecting Metro effluent has been upgraded from chlorination/dechlorination to an ultraviolet disinfection system.

The 2009 results document the continued significant improvements in Onondaga Lake brought about by these reductions in ammonia and phosphorus inputs from Metro. Water quality has improved dramatically; nutrient levels are reduced and dissolved oxygen has increased. No algal blooms were evident; the lake water was generally clear and aesthetically appealing. Total phosphorus concentrations averaged 17 µg/L over the summer of 2009 in the lake’s upper waters, comparable to conditions in nearby Oneida Lake and several of the Finger Lakes. The summer of 2009 marks the second consecutive year that the total P concentration in Onondaga Lake waters has complied with the state’s guidance value of 20 µg/L, which was established to protect recreational uses and drinking water supply. Bacteria counts in the Class B segment of the lake shoreline remained within limits set for water contact recreation. Ammonia N concentrations have been in full compliance with NYS standards in the lake’s upper waters since 2004, and at all water depths since 2007.

Clearer water allows light to penetrate deeper into the lake, and fosters the proliferation of macrophytes (rooted aquatic plants and bottom-dwelling algae) in nearshore shallow waters, to a water depth of six meters. The macrophyte community has also become more diverse, as more species of plants have colonized the nearshore waters of the lake. As these macrophyte beds have spread around the perimeter of the lake, they have brought improved habitat conditions. The populations of gamefish such as largemouth and smallmouth bass have increased steadily since 2000.

The 2009 report highlights an expanded review of the lake’s fish community, tracking changes over a full decade of AMP biological monitoring (2000 – 2009). Overall, there has been an increase in the quantity and quality of habitat, both littoral and pelagic, available to fish species. This has resulted in a slight increase in the number of species present and a more even distribution of fish throughout the lake. Many fish species, particularly those associated with vegetated habitats, are also increasing in abundance. The aquatic food web within the lake continues to include new species, both native and non-indigenous (exotic), with increasingly complex pathways of material and energy transfer among the life stages of the biota. This increasing complexity with regard to energy sources and energy flow results in an ecosystem that may be more resilient to environmental stress. The results of the 2009 AMP indicate that this is an ongoing process and that more changes are likely to occur. As lake water quality continues to improve, resulting in more diverse and higher quality habitat conditions, increases in aquatic species diversity, abundance, and interrelatedness can also be expected.

Segments of streams flowing into Onondaga Lake also exhibit degraded water quality and habitat conditions. The ACJ has required investment in improvements to the wastewater collection infrastructure as well as at Metro. These improvements are improving water quality and habitat conditions in segments of the lake tributaries affected by combined sewer overflows. Four strategies have been employed to eliminate wet weather discharges from the combined sewer system; these methods include separating sewers, constructing regional treatment facilities, capturing floatable materials and maximizing system storage capacity. During 2009, County facilities and other urban areas began to implement green infrastructure solutions to help manage urban storm runoff. Green infrastructure encourages infiltration, capture and reuse of storm runoff before it enters the sewer system. By preventing storm water runoff from entering the combined sewers, more capacity is available for sanitary sewage flow to reach Metro for treatment. The fourth stipulation includes specific requirements and milestone dates for capturing an increasing percentage of the annual stormwater volume. A “Save the Rain” initiative is underway to educate watershed residents about ways to capture and use rain water.

Water quality conditions in the Seneca River during 2009 were comparable to those measured in previous years. Although the proliferation of dreissenid mussels continues to affect water quality conditions, relatively high stream flows during the summer of 2009 prevented prolonged conditions of low dissolved oxygen. Ammonia and nitrite concentrations in the monitored segments of the Seneca River were in compliance during 2009.

Onondaga County Department of Water Environment Protection, in consultation with NYSDEC and the Onondaga Lake Technical Advisory Group, has developed a suite of metrics to help organize and report on the extensive AMP data set each year. These metrics relate to the lake’s designated “best use” for water contact recreation, fishing and protection of aquatic life. The 2009 results (Table EX-1) document substantial progress toward attaining the designated uses in Onondaga Lake.

Table EX-1. Summary of 2009 Onondaga Lake Conditions.
Restoration Goal	Measured By	2009 Results	Significance
Suitability for Water Contact Recreation
Indicator bacteria	Fecal colilform bacteria abundance	Met NYSDEC standards for water contact recreation in Class B segments (200 cfu/ 100 mL, geometric mean of at least 5 samples/month)	Class B segments of the lake exhibit water clarity and bacteria levels that would support swimming, boating, waterskiing and other types of contact recreation. Class C segments of the lake, which are close to the major tributaries, periodically exhibit elevated bacteria and reduced water clarity conditions after storms.
Water clarity	Secchi disk transparency (nearshore stations)	Met NYS Dept. of Health swimming safety guidance value (1.2 m water clarity) for water contact recreation in Class B segments
Aesthetic Appeal
Water clarity	Secchi disk transparency (mid-lake station)	Average June – Sept Secchi disk, South Deep (mid-lake station): 3.2 m	Total phosphorus (total P) concentration in the lake’s upper waters during summer (June- Sept) 2009 was 17 ug/L, within the NYSDEC guidance value of 20 ug/L established to protect the aesthetic quality of lakes and ensure their suitability for recreational use. The low total P resulted in low algal abundance and clear water. The lake was free of nuisance algal blooms, and cyanobacteria abundance was very low.
Algal blooms	Chlorophyll-a Total phosphorus in the upper waters, June – Sept	June – Sept chlorophyll-a @ South Deep (mid-lake station): 5.9 ug/L Low algal abundance throughout the entire recreational period, no blooms Summer average TP: 17 ug/L
Algal community structure	Abundance of cyanobacteria (blue-green algae)	<1% of the algal community was comprised of cyanobacteria
Aquatic Life Protection
Ammonia	Measured in-lake concentrations, year-round, all depths	100% of measurements met NYS standards, all depths	The 2009 water quality conditions fully support a diverse warm water aquatic biota. Prior to the ACJ improvements to the wastewater collection and treatment system, elevated concentrations of ammonia and nitrite N, and low concentrations of DO during fall mixing, were measured in Onondaga Lake. These water quality parameters are now in full compliance with ambient water quality standards established to protect even the most sensitive species and life stages.
Nitrite	Measured in-lake concentrations, year-round, all depths	100% of measurements met NYS standards, all depths
Dissolved oxygen (DO)	In-situ buoys and frequent field profiles during fall mixing (turnover), when historically conditions in Onondaga Lake have been most stressful to aquatic life	7.2 mg/L average DO during fall mixing, minimum 6.9 mg/L
Sustainable Recreational Fishery
Habitat quality	Cover and density of aquatic plants (macrophytes) Deep water dissolved oxygen during stratified period	Approximately 50% of the littoral zone exhibited dense macrophyte growth. The littoral zone is defined as the nearshore area where light reaches the sediment surface and is thus suitable for the growth of rooted aquatic plants. Summer anoxia in hypolimnion	Coverage in this range provides high quality habitat for fish reproduction and rearing; current conditions are near-optimal for smallmouth and largemouth bass. Lack of well-oxygenated cold water limits habitat for resident cold water fish community.
Fish reproduction	Reproduction of target species: · bass and sunfish · yellow perch · black crappie · rock bass · walleye and northern pike	Occurring: · bass and sunfish · yellow perch · rock bass No evidence: · black crappie · walleye · northern pike	Fish reproduction for several target species has not been observed in the lake. Adult populations of these species are stable and, in some cases, increasing. The lack of suitable spawning habitat, not water quality, appears to be the limiting factor in fish reproduction in the lake. Restoration of habitat is underway as part of the Honeywell lake cleanup project.
Fish community structure	Percent of fish species intolerant or moderately intolerant of pollution	4%	Most of the Onondaga Lake fishes are warm water species, and are relatively tolerant of pollution. Consequently, the percentage of fish species intolerant or moderately intolerant of pollution is unlikely to exhibit a large increase in the future.

1. Introduction to the AMP

1.1 Regulatory Requirements

The 2009 Annual AMP report has been prepared and submitted to the New York State Department of Environmental Conservation (NYSDEC) to comply with a judicial requirement set forth in the 1998 Amended Consent Judgment (ACJ) between Onondaga County, New York State and Atlantic States Legal Foundation. The ACJ, signed in 1998, has been modified four times, most recently by stipulation in November 2009. The ACJ requires a series of improvements to the County wastewater collection and treatment infrastructure, and an extensive monitoring program to document the improvements achieved by these measures. Onondaga County Department of Water Environment Protection monitors the quality of Onondaga Lake, the lake tributaries, and a segment of the Seneca River as part of the Ambient Monitoring Program (AMP); the program is focused on evaluating compliance with ambient water quality standards, the nature of the aquatic habitat, and trends toward improvement.

The NYSDEC is responsible for managing water resources throughout NY State. As part of this responsibility, NYSDEC classifies surface waters, including lakes, rivers, streams, embayments, estuaries and groundwater with respect to their best use. Monitoring results are evaluated on a regular basis to determine whether designated uses are supported, and if not, the factors precluding use attainment. Onondaga Lake was included on the state’s inaugural listing of impaired waters in 1998 due to its elevated levels of ammonia, phosphorus and bacteria, and for its low concentrations of dissolved oxygen (DO) in the upper waters during fall mixing. The NYSDEC most recent listing of impaired waters includes several segments of tributaries to Onondaga Lake. Waterbodies are placed on this list when there is evidence that water quality conditions are not in compliance with applicable standards, and/or the water bodies do not support their designated use.

Water flows to Onondaga Lake from a large land area drained by multiple tributaries, as illustrated in Figure 1-1. Several outfalls of treated municipal and industrial wastewater and stormwater also flow into the lake; Tributary 5A and the East Flume flow into Onondaga Lake along its western shoreline, and Metro effluent enters the lake at the southern shoreline. The locations of these three inflows are shown in Figure 1-2.

Onondaga Lake and its tributaries are currently classified to include Class B and Class C waters. The best usages of Class B waters are primary and secondary water contact recreation and fishing. Primary water contact recreation includes activities that immerse the body in the water, such as swimming; secondary water contact recreation includes activities without full immersion, such as boating. In addition, Class B waters shall be suitable for fish, shellfish, and wildlife propagation and survival. The best usage of Class C waters is fishing. These waters shall also be suitable for fish, shellfish and wildlife propagation and survival. Class C waters shall be suitable for primary and secondary water contact recreation, although other factors may limit the use for these purposes.

For many years, Onondaga Lake did not support its designated uses due to excessive discharges of municipal and industrial wastewaters and uncontrolled storm water runoff. Swimming was banned in 1940 due to elevated bacteria counts and poor water clarity. Conditions for aquatic life were compromised by high ammonia concentrations and low dissolved oxygen. Fishing was banned in Onondaga Lake in 1972 because of mercury contamination. The ban was lifted in 1986 and modified into a “catch and release fishery”; that is, recreational fishing was permitted but possession of lake fishes was not. Further modifications to the fish consumption advisories and regulations have occurred over the years, and there is no longer a blanket restriction on possession of all fish. The current advisory sets forth consumption limits on specific species, and includes the warning that women under age 50 and children under age 15 should not consume fish from Onondaga Lake. Everyone else is advised to eat no walleye of any size, nor largemouth or smallmouth bass over 15 inches. New in 2010 is the advisory to not eat any carp, channel catfish or white perch from Onondaga Lake. The specific advisory for Onondaga Lake also applies to tributaries and connected waters if there are no barriers to passage, such as dams or falls.

Table 1-1. Summary of Current Fish Consumption Advisories for Onondaga Lake.
Lake	Species	Advisory	Chemicals of Concern
Onondaga Lake	Largemouth bass and smallmouth bass over 15" and walleye	Don't eat	Mercury, PCBs
	Carp, channel catfish and white perch	Don't eat	PCBs, Mercury, Dioxin
	All fish not listed	Eat up to one meal per month	Mercury, PCBs
	Brown bullhead and pumpkinseed	Eat up to four meals per month	Mercury, PCBs

Some areas of Syracuse are served by combined sewer systems which carry both sewage and storm water in a single pipe. These pipes can overflow during periods of heavy rain and snowmelt, allowing a mixture of stormwater and untreated sewage to flow into creeks and ultimately reach Onondaga Lake. The sewer system was originally designed to overflow to prevent sewage from backing up into streets and basements, thereby protecting public health. The combined sewer overflows (CSOs) direct bacteria, floating trash, organic material, nutrients and solid materials to the waterways.

A comprehensive program to address the sources of pollution that preclude attainment of the designated uses is underway. Onondaga County, New York State Department of Environmental Conservation (NYSDEC) and Atlantic States Legal Foundation entered into the 1998 Amended Consent Judgment (ACJ) to resolve a lawsuit filed against Onondaga County alleging violations of the Clean Water Act; namely, that discharges from the Syracuse Metropolitan Wastewater Treatment Plant (Metro) were in violation of the facility’s discharge permit, and the combined sewer overflows (CSOs) did not comply with state and federal regulations. The ACJ has been modified over the years to respond to new technologies and actual water quality conditions. As of 2010, the County is required to undertake a phased program of wastewater collection and treatment improvements extending through 2018 (Tables 1-1 and 1-2).

Table 1-2 Metro Compliance Schedule. (ppd = pounds per day; mg/L = milligrams per liter)
Parameter	SPDES Limit	Effective Date	Achieved Date
Ammonia	Stage I : 8,700 ppd (7/1-9/30) 13,100 ppd (10/1-6/30)	January 1998	January 1998
	Stage II: 2 mg/L (6/1-10/31) 4 mg/L (11/1-5/31)	May 2004	February 2004
	Stage III: 1.2 mg/L (6/1-10/31) 2.4 mg/L (11/1-5/31)	December 2012	February 2004
Total Phosphorus	Stage I : 400 ppd (12-month rolling average)	January 1998	January 1998
	Stage II: 0.12 mg/L (12-month rolling average)	April 2006	April 2006
	Revised Interim Stage II: 0.10 mg/L (12-month rolling average)	November 2010	Pending
	Stage III: 0.020 mg/L (or as modified by TMDL)	December 2015 (or as modified by TMDL)	Pending

Table 1-3. CSO Compliance Schedule.
Project Phase	Goal	Effective Date
Stage I	Capture for treatment or eliminate 89.5% of combined sewage* during precipitation, within the meaning of EPA’s National CSO Control Policy	Dec 31, 2013
Stage II	Capture for treatment or eliminate 91.4% of combined sewage during precipitation, within the meaning of EPA’s National CSO Control Policy	Dec 31, 2015
Stage III	Capture for treatment or eliminate 93% of combined sewage during precipitation within the meaning of EPA’s National CSO Control Policy	Dec 31, 2016
Stage IV	Capture for treatment or eliminate 95% of combined sewage during precipitation within the meaning of EPA’s National CSO Control Policy	Dec 31, 2018
*on a system-wide annual average basis (per fourth stipulation to ACJ, Nov. 2009)

There are three elements to the ACJ: (1) improvements to Metro, primarily to reduce phosphorus and ammonia loading, (2) improvements to the wastewater collection infrastructure to reduce combined sewer overflows (CSOs); and (3) monitoring the surface waters to evaluate the effectiveness of the improvements to the wastewater collection and treatment system. Onondaga County has designed the AMP to provide the data and information needed to document the effectiveness of the controls on the municipal pollution sources. NYSDEC reviews and approves the annual AMP work plan, participates in technical work group meetings and reviews and approves the annual report.

The industrial pollution impacts are also being addressed; projects to intercept and treat contaminated groundwater, remove contaminated sediments and restore habitat are underway. This effort is spearheaded by Honeywell International with oversight by state and federal officials. A detailed description of the Honeywell remedial projects planned for the Onondaga Lake watershed is on the NYSDEC web site http://www.dec.ny.gov/chemical/48828.html.

1.2 Ambient Monitoring Program Design

The AMP is designed to identify sources of materials (nutrients, sediment, bacteria and chemicals) to the lake, evaluate in-lake water quality conditions, and examine the interactions between Onondaga Lake and the Seneca River. Representative samples are collected by trained field technicians from a network of permanent sampling locations along the lake tributaries, nearshore and deep stations in Onondaga Lake, and along the Seneca River (Figure 1-2). Data are evaluated with respect to compliance with water quality standards and trends.

In addition to the water quality monitoring effort, the AMP examines the health of the lake ecosystem by sampling fish, phytoplankton, zooplankton, benthic invertebrates, aquatic plants and dreissenid (zebra and quagga) mussels. The health of the watershed is assessed as well, through an integrated program that focuses on identifying potential sources of materials such as nutrients, sediment and bacteria. Biological indicators of stream condition are evaluated as well. A Data Analysis and Interpretation Plan (DAIP) (Table 1-3) guides program design and is a component of the annual workplan, and consequently subject to NYSDEC review and approval.

A rigorous Quality Assurance/Quality Control program is in place. The AMP workplan is subject to NYSDEC review and approval each year. Samples are collected by trained technicians and analyzed in a laboratory certified by the NYS Department of Health. Internal and external audits are conducted, blanks and duplicates are evaluated, and the results are presented in the annual AMP report. Experts serving on the Onondaga Lake Technical Advisory Committee (OLTAC) review the data and interpretive reports each year and make recommendations.

An expert on statistics and lake water quality periodically reviews the AMP design for its power to detect trends. That is, what sampling frequency and duration are needed to differentiate a significant change, given the magnitude of natural variation? This analysis, referred to as the Statistical Framework, has been completed for water quality and biological parameters by Dr. William W. Walker, a member of OLTAC. Dr. Walker’s evaluations of the AMP are available on his web site www.wwwalker.net/onondaga.

Each year, OCDWEP tests over 20,000 water samples and examines several thousand biological samples. The County has invested in the creation of custom databases to facilitate analysis and reporting. The 2009 data have been appended to the water quality database, which is a repository of tributary (T), lake (L) and river (R) data collected since 1968. An integrated biological database is used to manage results of the fisheries, phytoplankton, zooplankton, macroinvertebrate and macrophyte monitoring efforts.

Table 1-4. Data Analysis and Interpretation Plan.

Parameters	Sampling Locations	Compliance	TMDL Analysis	Trend Analysis	Trophic Status	Load Analysis	Model Support	Use Attainment	Effectiveness of CSO control measures	Indicator of Water Clarity	Nutrient Cycling	Habitat Conditions	Lake Ecology
Chemical
Alkalinity	L, T
Bacteria	L, T
BOD-5	L, T, R
Carbon	L, T, R
Cyanide	T
Mercury	L, T
Metals/Salts	L, T, R
Nitrogen	L, T, R
Phosphorus	L, T, R
Dissolved Silica	L,T
Solids	L, T, R
Sulfides	L
Dissolved Oxygen	L, T, R
Salinity	L, T, R
Physical
Conductivity	L, T, R
LiCor illumination	L, R
Secchi transparency	L, R
Turbidity	L, T, R
Biological
Chlorophyll-a/algae	L, R
Zooplankton	L
Macrophytes	L
Macroinvertebrates	L, T
Fish	L
Dreissenid mussels	L,R
Locations: L = Lake; T = Tributaries; R = Seneca River.

1.3 Turning Data into Information: Metrics

A series of metrics, defined as quantifiable physical, chemical and/or biological attributes of the ecosystem that respond to human disturbances, is used to help organize the extensive AMP dataset (Table 1-5). For the Onondaga Lake watershed, metrics are used to indicate progress towards compliance and attainment of the designated best use. Four categories address both human uses and ecosystem function: (1) water contact recreation; (2) aesthetics; (3) aquatic life protection; and (4) sustainable recreational fishery. Note that the 2009 evaluation of lake conditions with respect to the selected metrics is included in the Executive Summary (refer to Table EX-1). The water quality parameters in this table are those attributed to the discharges from Metro and the CSOs, as set forth in the ACJ. In addition to these central indices, additional water quality parameters are monitored in the lake, the tributary streams, and a segment of the Seneca River in order to improve stakeholders’ understanding of ecosystem functioning and compliance with other standards not directly related to wastewater (as summarized in Table 1-4).

Table 1-5. Summary of metrics used to evaluate progress toward improvement.
Metrics	Measured By	Target Levels
Suitability for Water Contact Recreation
Indicator bacteria	Fecal coliform bacteria abundance	100% of E. coli and fecal coliform bacteria (monthly geometric means of at least 5 observations) in compliance with water quality standards. Lake: compliance is measured during the Metro disinfection period (April 1 to October 15). Tributaries: compliance is measured year-round.
Water clarity	Secchi disk transparency (nearshore, Class B)	Lake: 100% of water clarity measurements greater than 4 ft. (1.2 m) between June and September, which is the NYS swimming safety guidance value.
Aesthetic Appeal
Water clarity	Secchi disk transparency (open waters South Deep)	Lake: 100% of water clarity measurements greater than 5 ft. (1.5 m) between June and September, which indicates conditions that are aesthetically appealing for recreational uses (swimming and boating).
Algal blooms	Chlorophyll-a concentrations: frequency, magnitude and duration of elevated levels	Lake: 85% of chlorophyll-a measurements less than 15 µg/L between June and September (below a threshold of algal abundance imparting a distinct greenish tinge to the water).
		Lake: 90% of chlorophyll-a measurements less than 30 µg/L between June and September (below a threshold of algal abundance associates with a nuisance algal bloom).
Algal community structure	Identification and enumeration of phytoplankton samples	Lake: Less than 10% of algal community biomass represented by cyanobacteria (blue-green taxa).
Aquatic Life Protection
Wastewater- related parameters	Ammonia N and nitrite concentrations, profiles through lake water column, biweekly program in tributaries	Lake and tributaries: 100% of annual measurements in compliance with standards designed to protect aquatic life.
Dissolved oxygen (DO)	Profiles through lake water column, annual biweekly program in tributaries	Lake and Tributaries: Daily average concentrations above 5 mg/L; Instantaneous minimum concentration above 4 mg/L. In NY, hypolimnetic anoxia in lakes during stratification is not enforced as a violation of ambient water quality standards, due to the challenges associated with defining natural conditions vs. cultural eutrophication.
Other chemical parameters listed in Table 1-4 (e.g., heavy metals)	Profiles through lake water column, annual biweekly program in tributaries	Lake and tributaries: 100% of annual measurements in compliance with standards designed to protect aquatic life.
Sustainable Recreational Fishery
Habitat quality	Aerial photograph interpretation of macrophyte cover	Lake: At least 40% of the littoral zone supports abundant macrophyte cover, based on optimal habitat for largemouth bass.
Fish species successfully reproducing	Nesting surveys, larval sampling, young-of-year sampling (littoral and pelagic) adult surveys	Lake: Reproduction of target species as specified in the Amended Consent Judgment · largemouth bass, smallmouth bass and sunfish · yellow perch · black crappie · rock bass · walleye and northern pike
Community structure	Percent of fish species intolerant or moderately intolerant of pollution	Lake: Increasing presence of fish species sensitive to pollution.

1.4 Mathematical Modeling

Monitoring data provide a means to evaluate current conditions, compliance and trends. Monitoring data also serve to test hypotheses and elucidate important processes and interactions affecting water quality and aquatic habitat. However, projecting future conditions in response to changing inputs and environmental conditions remains a significant challenge. Projecting future conditions requires models; the most robust models are constructed using data generated by a well-designed monitoring program.

In recognition of the need to project future water quality and habitat conditions, the ACJ requires development, calibration and confirmation of mathematical models using the extensive AMP data to support decisions related to Onondaga Lake improvement projects. Specifically, the models will provide critical information needed to manage the lake and its watershed, including the following:

· An understanding of the mechanisms underlying observed trends in the water quality of the lake;

· A projection of the benefits of Metro upgrades and CSO abatement measures;

· A more complete assessment of the assimilative capacity of the Seneca River and its ability to accept diverted Metro effluent as well as the impact of such a potential diversion on lake water quality;

· A projection of the benefits of any proposed watershed best management practices (BMPs);

· Development of total maximum daily loads (TMDLs) for phosphorus in the lake and support the development of a TMDL for dissolved oxygen in the Seneca River.

A suite of three integrated mathematical models are near completion:

Ø The Onondaga Lake Basin Model, developed by the US Geological Survey (USGS) in cooperation with the OLP, is designed to simulate the flow of water and materials (nutrients and sediment) to the lake;

Ø The Onondaga Lake Water Quality Model (OLWQM), developed by Anchor QEA, is a mechanistic model focusing on eutrophication; and

Ø The Three Rivers Water Quality Model (TRWQM), developed by Anchor QEA, is a mechanistic model focusing on dissolved oxygen conditions in the Seneca River.

These models are designed to quantify the response of Onondaga Lake and the Seneca River to improvements in wastewater treatment and non-point source pollution control measures within the watershed. The three models are integrated, with output from one providing input to the next. The Onondaga Lake Basin Model was developed by the USGS and calibrated using AMP data. The basin model supports a quantitative analysis of how land use changes in the lake’s watershed affect the water, nutrients, and sediment in runoff to Onondaga Lake. Managers can apply this model to estimate the potential effectiveness of various control strategies such as changing development patterns, or implementing best management practices in particular areas. The USGS basin model can also be used to evaluate the need for measures such as stormwater retention basins to mitigate peak runoff rates. Projected tributary flows and loads from the Onondaga Lake Basin Model will be used as input to the OLWQM to forecast the lake response to watershed measures, thus providing linkage between the models.

The OLWQM and TRWQM forecast how Onondaga Lake and the Seneca River respond to inputs of water and materials. These coupled Anchor QEA models will be used to evaluate the potential environmental benefits realized by diverting the Metro outfall or achieving the Stage III phosphorus limit. In addition to providing managers with the tools to determine the level of treatment and point of discharge from Metro, the two mechanistic models developed by Anchor QEA are supporting similar evaluations of other Onondaga County wastewater treatment plants discharging to the Seneca River, including the Wetzel Rd. and Baldwinsville-Seneca Knolls facilities. Onondaga County also works with Dr. William Walker to support the AMP design and data analysis and interpretation tasks. Dr. Walker developed a mass-balance framework to track the input, output and retention of materials (such as phosphorus) in Onondaga Lake. This framework uses hydrologic and water quality data collected in the lake and its tributaries since 1986. Results provide a basis for three tasks:

1. Estimating the magnitude of loads and precision of load calculations from each source;

2. Assessing long-term trends in load and inflow concentration from each source and source category (point, nonpoint, and total);

3. Evaluating the adequacy of the monitoring program, based upon the precision of loads computed from concentration and flow data.

Reports on these efforts are available at http://www.wwwalker.net/onondaga.

1.5 Timeline of Onondaga Lake and Watershed Events, 1998-2009

2. Onondaga Lake and its Watershed

The Onondaga Lake watershed encompasses approximately 285 square miles almost entirely within Onondaga County, including six natural sub-basins: Onondaga Creek, Ninemile Creek, Ley Creek, Harbor Brook, Bloody Brook and Sawmill Creek (refer to Figure 1-1). Tributary 5A and the East Flume direct runoff and industrial discharges into the lake. Much of the annual volume of treated wastewater flowing to Onondaga Lake though the Metro treatment plant originates outside of the watershed; water supply for the City of Syracuse is drawn from Skaneateles Lake, and for suburban towns and villages, Lake Ontario. The outlet of Onondaga Lake flows north to the Seneca River and ultimately into Lake Ontario. Onondaga Creek is the largest water source to the lake, followed by Ninemile Creek, Metro, Ley Creek and the smaller tributaries (Figure 2-1).

Figure 2-1. Hydrologic input to Onondaga Lake, as percent of total. Source: OCDWEP database.

Compared with other lakes in the Seneca-Oneida-Oswego river basin, the watershed of Onondaga Lake is more urbanized, as displayed in Figure 2-2, a map of land cover within the watershed. Approximately 28% of the land cover is classified as developed (urban/suburban), 51% as forested or scrub/shrub, and 9.5% as cultivated lands or pasture, with the remaining 12% comprised of wetlands, lakes, and barren land. Urban areas of the City of Syracuse, two towns and two villages border the lake.

Onondaga Lake is relatively small (Table 2-1). The shoreline is highly regular with few embayments. The majority of the shoreline is owned by Onondaga County and is maintained as part of a popular park and trail system. The parklands are used for recreational activities, shoreline fishing and cultural entertainment. The lake is increasingly popular for boating; sailboats, motorboats, kayaks and canoes are familiar sights on summer days. Local and regional fishing tournaments attract anglers to the lake and shoreline each year.

Table 2-1. Morphometric characteristics of Onondaga Lake.
Characteristic	Metric units	English units
Watershed area	738 km^2	285 mi^2
Lake:
Surface area	11.7 km^2	4.5 mi^2
Volume	131 x 10^6m^3	35 billion gallons
Maximum length	7.6 km	4.7 mi.
Maximum width	2 km	1.2 mi.
Maximum depth	19.5 m	64 ft.
Average depth	11 m	36 ft.
Average elevation*	111 m	364 ft.
Average flushing rate	4 times/yr.
*Elevation is of the lake surface, referenced to mean sea level.

3. Tributary Results: 2009 Water Quality Status and Trends

The 2009 water quality data indicate continued progress toward compliance with ambient water quality standards and restoration of designated uses. In this section, results of the 2009 monitoring effort are summarized and compared with historical data.

3.1 Climatic Conditions

Each year, the tributaries convey surface runoff and groundwater seepage from the large watershed toward Onondaga Lake. The volume of runoff, and consequently streamflow, varies each year depending on the amount of rainfall and snow cover. Overflows from the combined sewer system also vary in response to the intensity and timing of rainfall events, and, to a lesser degree, snowmelt. The Metro effluent volume exhibits less annual variation, although the effects of extreme wet or dry years can be detected due to the portion of the service area served by combined sewers.

Overall, 2009 was a dry year in Syracuse; the total precipitation of 35.36 inches was below the 30- year average (1979 – 2008) of 38.01 inches. The winter was snowy, however (146 inches compared to the average 121 inches), and June was extremely wet. Despite these variations, the average 2009 precipitation and temperature patterns were not inconsistent those measured over the previous 30 years. The climatic conditions were reflected in the streamflow conditions; streamflow conditions in the major tributaries remained close to long-term average conditions, with spikes in late winter and June, and additional spikes in response to late summer storm events.

3.2 Tributary Water Quality and Annual Loads

Compliance with Ambient Water Quality Standards

Several segments of Onondaga Lake’s tributary streams have been placed on the NYSDEC compendium of impaired waters, most recently updated in 2010. Waterbodies are placed on this list when there is evidence that water quality conditions are not in compliance with applicable standards, and/or the water bodies do not support their designated use. Results of the County’s AMP are among the primary data sets used to evaluate compliance. The 2009 tributary data indicate that the major tributaries are generally in compliance with standards, (Table 3-1) with some exceptions; the 2009 findings were consistent with those of previous years. Ley Creek continues to exhibit periodic exceedances of the ambient water quality standard for cyanide. Tributary 5A, which receives treated industrial wastewater from Crucible Specialty Metals, does not meet the copper standard. The East Flume exceeded the ambient water quality standards for mercury, pH, nitrite and ammonia on a regular basis during 2009. Monitoring for fecal coliform bacteria abundance in the tributaries was not frequent enough to evaluate compliance with the standard, which is expressed as the geometric mean of a minimum of five observations each month. Beginning in April 2010, Onondaga County increased sampling frequency in the tributaries to enable assessment of compliance with the ambient water quality standard for fecal coliform bacteria.

Table 3-1. Percent of Onondaga Lake tributary sample results in compliance with NYS water quality standards, 2009.
Monitoring Site	Ammonia-N	Arsenic	Cadmium	Chromium	Copper	Cyanide	Dissolved Oxygen*	Fecal Coliform**	Lead	Mercury***	Nickel	Nitrite	pH	Zinc
Ninemile Creek at Lakeland	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	96%	100%
Harbor Brook at Hiawatha	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	96%	100%
Harbor Brook at Velasko	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	100%	100%
Onondaga Creek at Kirkpatrick	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	100%	100%
Onondaga Creek at Dorwin	100%	100%	100%	100%	100%	100%	100%>4 100%>5	67%	100%	--	100%	97%	98%	100%
Onondaga Creek at Spencer	--	--	--	--	--	--	100%>4 100%>5	0%	--	--	--	--	96%	--
Ley Creek at Park	100%	100%	100%	100%	100%	75%	100%>4 96%>5	--	100%	--	100%	100%	96%	100%
Tributary 5A at State Fair Blvd.	96%	100%	100%	100%	0%	100%	100%>4 85%>5	--	100%	--	100%	96%	92%	100%
Allied East Flume	38%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	0%	85%	100%
Onondaga Lake Outlet (2ft)	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	100%	100%
Onondaga Lake Outlet (12ft)	100%	100%	100%	100%	100%	100%	100%>4 92%>5	--	100%	--	100%	100%	100%	100%
Bloody Brook at Old Liverpool Road	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	100%	100%
Bloody Brook at Onondaga Lake Parkway	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	100%	100%
Sawmill at Onondaga Lake Rec. Area	100%	100%	100%	100%	100%	100%	100%>4 100%>5	--	100%	--	100%	100%	100%	100%
Notes: * Dissolved oxygen results shown for compliance with 4 mg/l (>4) and 5 mg/l (>5) standards. For nontrout waters, the minimum daily average shall not be less than 5.0 mg/L, and at no time shall the DO concentration be less than 4.0 mg/L (§703.3). ** Fecal coliform compliance based on monthly geometric mean from a minimum of 5 measurements; only those stations with a minimum of 5 measurements in the course of a given month were evaluated for compliance by this standard. ***Mercury method reporting limit (MRL) is 0.02 μg/l, which is two orders of magnitude greater than the compliance value of 0.0007 μg/l. 71% of the analytical results were below the limit of detection. Given this data set, one cannot ascertain whether mercury reported as non-detect to 0.02 μg/l was present in the samples at levels above the regulatory limit of 0.0007 μg/l; therefore an accurate percent compliance cannot be calculated.

Compliance with Metro SPDES Permit

Onondaga County was in full compliance with conditions of the State Pollution Discharge Elimination System (SPDES) permit regulating the volume and quality of effluent discharged from the Metro facility to Onondaga Lake through Outfall 001. There were four exceedances of permit limits on Outfall 002 (bypass) in 2009, two each for total residual chlorine and settleable solids.

Effluent ammonia N remained well below the seasonal limits of 1.2 mg/L (summer) and 2.4 mg/L (winter), as displayed in Figure 3-1. Phosphorus concentrations were also consistently low throughout 2009 (Figure 3-2). As discussed in Section 1, the 2009 amendment to the ACJ revised the interim Stage II TP effluent limit to 0.10 mg/L. Compliance with the revised interim limit, which is expressed as a 12-month rolling average, will be evaluated beginning in November 2010.

Flows and Loads

The 2009 flow-weighted average concentration of phosphorus, ammonia-N, TKN, total suspended solids, fecal coliform bacteria and chloride measured in the Onondaga Lake tributaries and Metro effluent are summarized in Table 3-2. For additional detail, including the relative standard error of the means, refer to the Library Table L05.2.1. Note that fully-treated Metro effluent exhibits phosphorus concentrations comparable to those of the natural tributaries. Approximately 97% of flow reaching Metro in 2009 received advanced treatment and entered the lake through Outfall 001; the remaining 3% received primary treatment and entered the lake through Outfall 002 (bypass). Fully-treated Metro effluent is also much less turbid (clearer) than water flowing to the lake from the natural tributaries. Harbor Brook exhibited the highest abundance of fecal coliform bacteria of all the tributaries during the biweekly monitoring program (which does not specifically target storms). Ninemile Creek, which does not receive CSOs, exhibited fecal coliform bacterial abundance comparable to that measured in Onondaga Creek and Ley Creek, which do receive CSOs.

Table 3-2. Flow-weighted average concentration of selected parameters, 2009, Onondaga Lake tributaries (with number of samples in parentheses).
Parameter* Units	TP mg/L	SRP mg/L	NH3-N mg/L	TKN mg/L	TSS mg/L	Chloride mg/L	Bacteria cfu/100ml
Metro Effluent **	0.080 (364)	0.003 (87)	0.28 (363)	1.2 (363)	5.5 (364)	499 (202)	829 (210)
Metro Bypass	1.13 (41)	0.15 (2)	5.9 (41)	10 (41)	56 (41)	615 (2)	270,226 (29)
Onondaga Creek	0.085 (26)	0.008 (26)	0.066 (26)	0.57 (26)	63 (26)	422 (26)	1,620 (26)
Ninemile Creek	0.069 (26)	0.010 (26)	0.22 (26)	0.73 (26)	30 (26)	268 (26)	2,178 (26)
Ley Creek	0.10 (26)	0.016 (26)	0.28 (26)	0.83 (26)	24 (26)	336 (26)	1,916 (26)
Harbor Brook	0.092 (31)	0.037 (31)	0.081 (26)	0.48 (31)	29 (31)	280 (31)	6,312 (32)
Tributary 5A	0.12 (26)	0.037 (26)	0.15 (26)	0.46 (26)	19 (26)	351 (26)	73 (26)
East Flume	0.11 (26)	0.030 (26)	0.90 (26)	1.4 (26)	11 (26)	570 (26)	110 (26)
Tributaries results are reported for downstream sampling locations closest to Onondaga Lake. Flow-weighted average concentrations were computed on each sampled day using instantaneous flows for Storm Event samples and daily mean flows for Routine samples. *TP = Total Phosphorus; SRP = Soluble Reactive Phosphorus; NH3-N = Ammonia as N; TKN = Total Kjeldahl Nitrogen; TSS = Total Suspended Solids; Bacteria = Fecal Coliform bacteria ** METRO effluent NH3-N, TP, and TSS based on daily measurements, Metro bypass is only sampled when active.

The 2009 loading of these selected parameters (Table 3-3) illustrates the importance of the relative flow volume on total external loading of nutrients, sediment, chloride and bacteria to the lake. The values presented in Table 3-3 are generated by a customized loading model that uses the detailed flow record and results of grab samples of water quality conditions; the significant figures in the table should not be interpreted as presenting the precision of the estimates. The percent of the total load attributed to each source is summarized in Table 3-4. Note that 2009 results for all measured parameters, and the standard error of the estimates, are presented in the library.

Table 3-3. Annual loading of selected water quality parameters, in metric tons (mt), to Onondaga Lake in 2009. Number of samples is shown in parentheses.
Parameter* Units	TP mt	SRP mt	NH3-N mt	TKN mt	TSS mt	Chloride mt	Bacteria 10^10 cfu
Metro Effluent (1)	6.5 (364)	0.21 (87)	23 (363)	94 (363)	450 (364)	40,567 (202)	67,319 (210)
Metro Bypass (2)	2.5 (41)	0.33 (2)	13 (41)	22 (41)	121 (41)	1,330 (2)	584,782 (29)
Onondaga Creek	13 (26)	1.3 (26)	10 (26)	89 (26)	9,896 (26)	66,414 (26)	254,682 (26)
Ninemile Creek	10 (26)	1.5 (26)	33 (26)	112 (26)	4,545 (26)	40,749 (26)	331,038 (26)
Ley Creek	3.7 (26)	0.59 (26)	10 (26)	30 (26)	891 (26)	12,271 (26)	69,878 (26)
Harbor Brook	0.88 (31)	0.36 (31)	0.77 (26)	4.6 (31)	277 (31)	2,676 (31)	60,306 (32)
Tributary 5A	0.17 (26)	0.052 (26)	0.21 (26)	0.65 (26)	27 (26)	492 (26)	103 (26)
East Flume	0.12 (26)	0.033 (26)	0.97 (26)	1.5 (26)	11 (26)	617 (26)	119 (26)
Tributaries results are reported for downstream sampling locations closest to Onondaga Lake. The flow-weighted-mean concentration is computed for each day before being used in computing loads. *TP = Total Phosphorus; SRP = Soluble Reactive Phosphorus; NH3-N = Ammonia as N; TKN = Total Kjeldahl Nitrogen; TSS = Total Suspended Solids; Bacteria = Fecal Coliform bacteria. (1) Metro Outfall 001 calculated loads of NH3-N, TP, TSS are based on daily measurements; METRO TKN based on 5 measurements/2 wks (2) Metro Bypass Outfall 002 estimates based on periodic grab samples when outfall is active (high flow events where the capacity of the treatment plant is exceeded).

Table 3-4. Percent annual loading contribution by gauged inflow, 2009.
Parameter*	TP	SRP	NH3-N	TKN	TSS	Chloride	Bacteria	Water
Metro Effluent	17%	4.8%	25%	27%	2.8%	25%	4.9%	18%
Metro Bypass	6.5%	7.5%	14%	6.3%	0.75%	0.81%	43%	0.49%
Onondaga Creek	36%	30%	11%	25%	61%	40%	19%	36%
Ninemile Creek	28%	34%	36%	32%	28%	25%	24%	35%
Ley Creek	9.7%	13%	11%	8.5%	5.5%	7.4%	5.1%	8.3%
Harbor Brook	2.3%	8.1%	0.85%	1.3%	1.7%	1.6%	4.4%	2.2%
Tributary 5A	0.46%	1.2%	0.23%	0.18%	0.16%	0.30%	0.008%	0.32%
East Flume	0.33%	0.75%	1.1%	0.42%	0.07%	0.37%	0.009%	0.25%
*TP = Total Phosphorus; SRP = Soluble Reactive Phosphorus; NH3-N = Ammonia as N; TKN = Total Kjeldahl Nitrogen; TSS = Total Suspended Solids; Bacteria = Fecal Coliform bacteria.

In 2006, OCDWEP and USGS initiated a joint project to enhance data collection at two sites on Onondaga Creek, to provide additional data regarding the influence of rural and urban watersheds on stream water quality:

• Route 20 in Lafayette, in the rural headwaters, and
• Spencer Street in Syracuse, in the urban area affected by CSO discharges.

A new gauging station was constructed at Route 20 in 2006, while an existing gauging station was upgraded at Spencer Street. In-situ water quality monitoring devices (sondes) and meteorological data collection capabilities were installed, including precipitation collection equipment outfitted with heating elements to measure snowfall precipitation water equivalents.

The following 2009 data files are included in the Library:

• USGS flow and precipitation
• In-situ sonde results for turbidity, temperature and dissolved oxygen.
• A summary of the precipitation that occurred on and within three days of sampling
• Laboratory analytical results
• The analytical results with the 3-day sum of precipitation for phosphorus and other parameters

Onondaga Creek tributary data were also used to evaluate contributions in 2009 from the rural land use characteristic of the tributary’s headwaters (Route 20 monitoring station), predominantly rural watershed (Dorwin Ave. monitoring station) and predominantly urban watershed (Spencer St. monitoring station), based on concentration, flow, instantaneous loading, and contributing area.

Storm Events

Storm event sampling is conducted periodically in addition to the biweekly monitoring program, in an effort to characterize peak flow and loading conditions. Events are initiated when the forecast predicts heavy rains; storms with rainfall of sufficient intensity to trigger the CSOs (at least 0.35 inches per hour) are targeted. DWEP field technicians collect samples at multiple locations and at frequent intervals during the storm and for up to 48 hours after it subsides.

Storm events are conducted as remedial projects are completed; results are compared with baseline (pre-improvement) data. Loads of fecal coliform bacteria, chloride, TP, SRP, total dissolved P (defined as all non-particulate P fractions), total suspended solids, and total Kjeldahl N (defined as organic N and ammonia) are calculated over the course of the storm. These results are added to the cumulative database of storm loads, and compared to tributary-specific baseline (pre-improvement) conditions, as a function of the total volume of storm flow. The hypothesis is that improvements to the collection system will result in reduced loading of fecal coliform bacteria and other wastewater-related parameters.

Water quality monitoring of Onondaga Creek was completed during one intense rainfall event in August 2009. The storm was of short duration (approximately 0.8 inches in one hour), and most of the samples were collected just after the peak flow, on the receding limb of the hydrograph, highlighting the challenge of responding to storm events and the potential value of automated sampling devices. The Midland Ave. Regional Treatment Facility (RTF) was completed in May 2008. After a one-year testing phase, Onondaga County DWEP began operation of the facility on May 15, 2009. This RTF was designed to capture and treat the mixture of storm water runoff and untreated sewage from three large CSOs. Information from the real-time supervisory control and data acquisition (SCADA) system indicated that some of the combined sewage volume (estimated at no more than 1.2 million gallons) was released to Onondaga Creek through the emergency overflow diversion during the August, 2009 event, due to a delay in activating the influent pumps. In addition, approximately 32,300 gallons were released to Onondaga Creek after disinfection. The remaining combined sewage volume was stored and pumped back to Metro for full treatment. OCDWEP prepares quarterly reports to NYSDEC with operational details for RTFs, flow control facilities and the Erie Boulevard Storage System (EBSS).

Given the short duration of the August storm, the total storm volume was relatively low compared with other events captured as part of the AMP. The total loading of fecal coliform bacteria, phosphorus and solids were comparable to the loading estimates from previous storm events.

Wet and Dry Weather Events

The concentration of fecal coliform bacteria present in the lake tributaries during wet weather is affected by stormwater runoff and overflow of the combined sewers. CSO remedial measures and improved stormwater management techniques are underway. Among the objectives of the AMP is a storm event monitoring program to track changes in bacterial concentrations and loading to Onondaga Lake during wet weather. Another objective is to track bacterial abundance during non-storm periods as a means of identifying any illicit connections of sanitary waste to the stormwater collection systems, or portions of the sewerage infrastructure in need of repair.

To help meet these two related objectives, bacterial quality of the CSO-affected streams is evaluated at both low flow and high flow conditions by segregating the data set based on antecedent precipitation over the 1990-2009 annual monitoring years. The total annual loadings of bacteria from the monitored inflows to Onondaga Lake were categorized based on whether a year was considered “dry” or “wet”. At this aggregated level, there is no apparent correlation between total annual loading and rainfall.

Both Harbor Brook and Onondaga Creek have stations upstream and downstream of the urban CSO-affected corridor. Comparing these upstream and downstream stations reveals changes in loading as the streams flow through the urban corridor. Ninemile Creek receives stormwater runoff from a separate sewer system. Examining the summer average concentrations categorized by low and high flows, it is clear that the fecal coliform concentrations are higher when flows are higher; also, that concentrations at stations downstream of CSOs are higher than at stations upstream of CSOs. Over time, the concentrations during summer low flow conditions are consistently higher downstream of CSOs than upstream. Since CSOs are not active during dry weather conditions, the higher concentrations observed downstream are not attributable to this source.

During 2009, higher fecal coliform concentrations observed in the tributaries were generally associated with wet weather conditions. As in the past, concentrations were typically higher at monitoring stations downstream of CSOs than upstream. Wet weather fecal coliform bacteria levels were notably elevated at the downstream station on Harbor Brook.

Trends

With the phosphorus reduction in Metro effluent achieved by the 2005 start-up of the advanced physical-chemical treatment process, the loading of phosphorus to Onondaga Lake has been significantly reduced (Figures 3-3, 3-4 and 3-5). The watershed is now the larger source of total and total soluble phosphorus to the lake. The decrease illustrated in Figures 3-3 and 3-4 are statistically significant, as summarized in Library Table L05.2.1. The strong relationship between the external phosphorus load and the summer average concentration at the South Deep station is illustrated in Figure 3-5.

Comparison of phosphorus loading before the ACJ (1990-1998) and after implementation of the ActiFlo system at Metro (2005-2009) indicates the magnitude of reduction in phosphorus loading realized by this technology (Tables 3-5 and 3-6).

Table 3-5. Tributary and Metro Total Phosphorus (TP) Loading to Onondaga Lake, pre-ACJ and post-ActiFlo implementation. (mt = metric tons; concentrations flow-weighted).
	1990-1998 (pre-ACJ)				2005-2009 (post-ActiFlo)
Location	Flow (%)	TP (mt)	TP (% Load)	TP (mg/l)	Flow (%)	TP (mt)	TP (% Load)	TP (mg/l)
Metro:
fully treated	21%	52	57%	0.56	18%	11	26%	0.12
bypass	0.94%	8.5	7.5%	1.8	0.36%	2.0	4.9%	1.2
Watershed:
Onondaga Creek	34%	20	19%	0.12	37%	14	34%	0.077
Ninemile Creek	32%	10	10%	0.065	34%	9.1	23%	0.055
Ley Creek	8.7%	5.7	5.8%	0.14	8.1%	3.5	8.7%	0.087
Harbor Brook	2.1%	0.71	0.71%	0.070	2.5%	1.1	2.8%	0.092
Tributary 5A	0.72%	0.17	0.19%	0.054	0.23%	0.13	0.31%	0.11
East Flume	0.23%	0.19	0.18%	0.20	0.17%	0.11	0.27%	0.14
Totals	100%	97	100%	--	100%	41	100%	--

Table 3-6. Tributary and Metro Soluble Reactive Phosphorus (SRP) Loading to Onondaga Lake, pre-ACJ and post-ActiFlo implementation. (mt = metric tons; concentrations flow-weighted).
	1990-1998 (pre-ACJ)				2005-2009 (post-ActiFlo)
Location	Flow (%)	SRP (mt)	SRP (% Load)	SRP (mg/l)	Flow (%)	SRP (mt)	SRP (% Load)	SRP (mg/l)
Metro:
fully treated	21%	12	59%	0.13	18%	0.74	12%	0.008
bypass	0.94%	2.5	9.7	0.50	0.36%	0.42	7.9%	0.24
Watershed:
Onondaga Creek	34%	3.3	16%	0.021	37%	1.6	30%	0.009
Ninemile Creek	32%	1.7	7.9%	0.011	34%	1.5	29%	0.009
Ley Creek	8.7%	1.4	6.1%	0.033	8.1%	0.55	11%	0.014
Harbor Brook	2.1%	0.25	1.1%	0.024	2.5%	0.43	8.5%	0.035
Tributary 5A	0.72%	0.030	0.17%	0.010	0.23%	0.034	0.65%	0.029
East Flume	0.23%	0.065	0.29%	0.092	0.17%	0.036	0.70%	0.046
Totals	100%	21	100%	---	100%	5.2	100%	---

In a similar manner, the improvements to Metro have resulted in a statistically significantly reduction in the input of ammonia-N to Onondaga Lake (Figure 3-6). Note that the total nitrogen in the effluent has remained relatively constant. The Biologically Aerated Filtration (BAF) process that came on-line in 2004 achieved year-round nitrification (biologically-mediated oxidation) of ammonia to nitrate-N. Prior to implementation of the BAF, Metro effluent (fully- treated discharge through Outfall 001 plus bypass) represented about 90% of the external ammonia loading to Onondaga Lake; both the percent contribution of Metro to the total load and the total load itself are now greatly diminished (Figure 3-7).

Tables summarizing a statistical analysis of the trends in concentrations and loading of parameters in addition to ammonia and total P are in the library.

4. Onondaga Lake: 2009 Water Quality Status and Trends

The AMP is designed to evaluate the response of Onondaga Lake to improvements implemented at the Metro facility and the CSOs. In addition, data are collected to evaluate other chemical parameters in the lake, including low-level mercury.

Samples are collected from nearshore sampling stations as well as two mid-lake stations. The South Deep mid-lake station is sampled with greater frequency; the North Deep station is sampled four times per year to confirm that water quality conditions measured at the South Deep station continue to be representative of mid-lake conditions.

4.1 Trophic State Indicator Parameters

Onondaga Lake can be characterized by its trophic status, that is, how much sunlight it converts to organic matter through photosynthesis. Highly productive systems are termed eutrophic, while systems with low levels of productivity are termed oligotrophic. Those in between are called mesotrophic. Excessive productivity can result in conditions that impair a waterbody for a particular use, such as water supply or recreation.

The productivity of Onondaga Lake, like most lakes in the Northeast, is limited by the availability of phosphorus. Adding phosphorus induces eutrophication, and such over-productive waters support an abundant community of algae and cyanobacteria (blue-green algae). Approximately 50 species of cyanobacteria have been shown to produce toxins that are harmful to vertebrates (Codd 1995).

When algal biomass settles to the lower, unlighted areas of a productive lake, its decay robs the lower waters of dissolved oxygen, making them uninhabitable by fish or other oxygen-requiring organisms. Under these anaerobic or oxygen-free environments, undesirable compounds such as ammonia and soluble phosphorus may be liberated from the sediments.

Monitoring the trophic status of impaired waters like Onondaga Lake involves tracking several key parameters to assess the type and abundance of algae, and the chemistry of the deep waters. Three primary trophic state indicator parameters are used to evaluate a lake’s trophic status and trends: total P, chlorophyll-a and Secchi disk transparency.

Total Phosphorus (TP)

Since the productivity of Onondaga Lake is limited by the availability of phosphorus in the water, total phosphorus concentration (TP) is an important indicator of trophic status. Phosphorus concentrations in the lake’s upper waters are in steep decline (Figure 4-1), averaging 17 µg/L over the summer of 2009, comparable to conditions in nearby Oneida Lake and several of the smaller Finger Lakes. The summer of 2009 marked the second consecutive year that the total P concentration in Onondaga Lake waters complied with the state’s guidance value of 20 µg/L, which was established to protect recreational uses.

Chlorophyll-a

One of the undesirable attributes of eutrophic waters is their green-tinged water and turbidity, or cloudiness, which is usually caused by the large populations of algae containing the photosynthetic pigment chlorophyll-a. The measurement of chlorophyll-a is, therefore, a more or less direct measurement of the turbidity of the water as well as an indicator of its productivity, since the amount of photosynthesis correlates strongly with the amount of chlorophyll-a in the water. The federal EPA and NYSDEC are developing nutrient criteria for lakes to protect water supply and recreational use, as well as deriving numerical limits on response variables such as chlorophyll-a. In the absence of state or federal criteria, the AMP has used site-specific criteria of 15 and 30 ug/L to screen algal bloom thresholds for Onondaga Lake; these values have not been promulgated and are not enforceable.

In Onondaga Lake, chlorophyll-a concentrations above 15 µg/L are associated with green-tinged and turbid waters that are less appealing for recreational use. Nuisance bloom conditions are defined as chlorophyll-a concentrations greater than 30 μg/L. There were no algal blooms in Onondaga Lake during the summer recreational period of 2009 (Figure 4-2). The average and peak concentrations of this plant pigment have declined significantly (Figure 4-3). Summer data are displayed to track suitability of the lake for recreational uses. The annual data provide additional information regarding peak concentrations of chlorophyll that may be associated with spring and/or fall algal blooms.

In lakes where phytoplankton abundance is limited by phosphorus, the two trophic state parameters are highly correlated. Data from regional lakes (Figure 4-4) illustrate this relationship. Data for the Finger Lakes represent results of a NYSDEC survey conducted between 1996 and 1999. NYSDEC rejected their phosphorus data from 1998 for quality control reasons. The NYSDEC study design called for sampling each Finger Lake monthly over the summer season at a single mid-lake station, with the exception of Cayuga Lake which was sampled at three locations (Callinan 2001). Oneida Lake data were supplied by the Cornell Biological Field Station (Lars Rudstam, personal communication, June 2010). Oneida Lake is notably shallower than the Finger Lakes and does not develop stable thermal stratification during the summer.

The progressive reduction in TP concentration in Onondaga Lake is illustrated in Figure 4-4, as is the extent to which recent conditions are comparable to those measured in regional lakes. Note that the measured chlorophyll-a concentration in Oneida Lake is lower than predicted from the regression of the Finger Lakes data. This is attributed to food web effects; many grazing organisms (for example, dreissenid mussels and larger zooplankton) can effectively keep algal abundance low. In contrast, the relatively elevated chlorophyll-a in Onondaga Lake in 2007, considering the lake’s TP concentration that summer, is likely a result of diminished grazing pressure. The alewife was highly abundant in 2007; this clupeid fish had virtually eliminated larger zooplankton species such as Daphnia sp., which are more efficient grazers of phytoplankton. In the absence of the grazing pressure from the larger zooplankton, the 2007 phytoplankton standing crop was relatively high.

Secchi Disk Transparency

Another—and more direct—indicator of turbidity of the water is the Secchi disk transparency. A Secchi disk is a 25 cm diameter disk with alternating black and white quadrants. It can be lowered into the lake, and the depth at which it can no longer be seen from the surface or from the deck of a boat, is known as the Secchi disk transparency. Greater depth indicates clearer and less productive waters. Highly productive waters may have Secchi disk readings of less than one meter. Water clarity data are influenced by both bottom-up (nutrient levels) and top-down (food web) effects; the presence and abundance of grazing organisms has a major impact on the algal community.

To meet swimming safely guidance, Secchi disk transparency greater than 1.2 m (4 ft) is required at designated beaches (see Table 4-2). There is no NYS standard or guidance value for Secchi disk transparency of off-shore waters; most lake monitoring programs in the state monitor Secchi disk transparency at a mid-lake station overlying the deepest water, comparable to Onondaga Lake South Deep station. The Citizens Statewide Lake Assessment Program (CSLAP),a joint effort of NYSDEC and the NYS Federation of Lake Associations, considers summer average Secchi disk transparency greater than 2 m as indicative of mesotrophic conditions (Kishbaugh 2009). The water clarity of Onondaga Lake was high in 2009, averaging 3.2 m over the four-month summer period, with periods in mid-summer exhibiting exceptional water clarity, approaching 6 m (Figure 4-5).

In addition to Secchi disk transparency, readings are made of light extinction using a LiCor data logger. These readings correlate with Secchi measurements.

Trophic State Index

The three trophic state indicator parameters can be expressed on a common scale, ranging from 1 to 100, with higher values indicating greater productivity (Carlson 1997). By all measures, the trophic state of Onondaga Lake has shifted dramatically, as demonstrated by reductions in the lake’s trophic state index, or TSI, (Figure 4-6) calculated from summer average total P, chlorophyll-a and Secchi disk transparency. The 2009 results confirm that Onondaga Lake has become less productive, and all three trophic state indicator parameters are now clearly in the mesotrophic range.

4.2 Ammonia and Nitrite

Until recently, Onondaga Lake was considered impaired by elevated concentrations of ammonia; concentrations of this potentially harmful form of nitrogen exceeded the state ambient water quality standard for aquatic life protection (Table 4-1). The lake is now in full compliance with ambient water quality standards for ammonia, and in 2008 was officially removed from the State’s 303(d) list of impaired waterbodies for this water quality parameter. In a similar manner, the measured concentrations of nitrite N were in compliance with the NYS ambient water quality standard for a warm water fish community during the 2009 monitoring period.

Table 4-1. Percent of Ammonia Measurements in Compliance with Ambient Water Quality Standards, Onondaga Lake, 1998-2009.
Depth	Percent measurements in compliance, NYS standard
(m)	1998	1999	2000	2001	2002	2003	2004*	2005	2006	2007	2008**	2009
0	64	62	86	95	68	96	100	100	100	100	100	100
3	45	67	90	90	68	96	100	100	100	100	100	100
6	50	86	90	95	73	100	100	100	100	100	100	100
9	41	76	90	95	73	100	100	100	100	100	100	100
12	18	52	90	81	50	80	100	100	100	100	100	100
15	23	52	57	52	41	56	80	100	100	100	100	100
18	23	48	52	38	32	48	75	95	95	100	100	100
* Advanced ammonia treatment came on line in early 2004 ** In 2008, Onondaga Lake was de-listed for ammonia impairment on the state 303(d) list

4.3 Recreational Quality

Recreational quality of Onondaga Lake is evaluated using two parameters: fecal coliform bacteria and water clarity. In New York, fecal coliform bacteria are used to indicate the potential presence of raw or partially treated sewage in water. Although most strains of fecal coliform bacteria are not harmful, this class of bacteria is present in the intestinal tract of all mammals; the presence and abundance of fecal coliform bacteria in water is correlated with the risk of encountering pathogenic (disease-causing) microorganisms, including bacteria, viruses and parasites. Abundance of these indicator bacteria in nearshore areas of Onondaga Lake is used to monitor compliance with ambient water quality standards and the attainment of contact recreational use.

Bacteriological data often vary by orders of magnitude due to the event-driven nature of the sources. For that reason, geometric means are best suited for examining spatial and temporal trends. Examining nearshore summer data collected since 1999 (Figure 4-7), it is clear that bacteria levels are consistently higher in the southern region of Onondaga Lake, close to the major inflows, as compared to the northern region. Bacteria levels at the Class B stations and the lake outlet are low, confirming that the fecal coliform bacteria do not persist in the lake environment long enough, and are sufficiently diluted, to be present in the northern stations at levels of potential concern to human health. The results displayed in these graphs include both routine samples and samples collected during and shortly after storm events.

The data in Figure 4-7 demonstrate trends and relative abundance of the indicator bacteria, but do not evaluate compliance with standards. The NY state standard for fecal coliform bacteria is assessed by taking frequent samples at each location, a minimum of five per month, and calculating the geometric mean of the results. The ambient water quality standard for fecal coliform bacteria, designed to protect human health during water contact recreation, is set at 200 cfu (colony-forming units) per 100 ml of lake water. The standard applies during the period of Metro disinfection, which is April 1^st – October 15^th. In 2009, the standard was met at all but one monitoring location. All stations in the Class B portion of the lake were in full compliance, as shown in Figure 4-8. Bacteria levels in portions of the lake typically increase after significant storm events. The occasional high bacteria levels is one reason why there are no designated bathing beaches on Onondaga Lake; the potential presence of industrial residuals in sediment is another consideration.

Water clarity is measured at the same network of near-shore stations. While there is no NYSDEC standard for water clarity, the NYS Department of Health (DOH) has a swimming safety guidance value for designated bathing beaches of 4 ft. (1.2 m). The 2009 results demonstrate that the DOH swimming safety guidance value was met throughout the summer recreational period (June 1^st - Sept 30^th).

Table 4-2. Nearshore Secchi disk transparency statistical summary for Onondaga Lake, 2009.
		Secchi Depth (m)^a				% Observations	% Observations	% Observations
Station	Location Description	N	Mean	Max	Min	>1.2m (Jun 1 to Sep 30)^b	on bottom, total^c	on bottom in <1.2m depth^d
Class C
Ninemile Creek	near mouth of Ninemile Creek	22	1.3	3.1	0.2	95%	86%	9.1%
Ley Creek	near mouth of Ley Creek	22	1.3	>1.5	0.9	90%	91%	9.1%
Metro	near mouth of Metro discharge	22	1.2	>1.5	>0.6	100%	100%	14%
Onondaga Creek	near mouth of Onondaga Creek	22	1.1	2.2	0.1	43%	5%	4.5%
Harbor Brook	near mouth of Harbor Brook	22	1.3	>1.5	>0.9	100%	100%	4.5%
Class B
Wastebeds	north of mouth of Tributary 5A	22	1.6	4.1	>1.2	100%	91%	0%
Maple Bay	north end of the lake, south of outlet	22	1.4	3.0	>1.1	100%	95%	4.5%
Willow Bay	north end of the lake, north of outlet	21	1.4	>1.7	>1.2	100%	100%	0%
Onondaga Lake Park	Onondaga Lake Park, north of marina	21	1.3	>1.5	>1	100%	100%	4.8%
Bloody Brook	near mouth of Bloody Brook	22	1.3	>1.5	>1	100%	100%	9.1%
^aStatistics include observations for which the Secchi disk was visible on the bottom of the lake in less than 1.2 m of water. The ">" ("greater than") symbol indicates the Secchi disk was visible on the bottom for this measurement. Sampling at the nearshore stations is standardized to an area of 1.2-1.5 m depth. ^bObservations >1.2 m are in compliance with swimming safety guidelines; the percent compliance does not include those measurements for which the Secchi disk was visible on the bottom of the lake in less than 1.2 m of water. ^c Percent of total observations at each location for which the Secchi disk was visible on the bottom of the lake. ^dPercent of total observations at each location for which the Secchi disk was visible on the bottom of the lake in less than 1.2 m of water.

4.4 Metro Improvements and Lake Response

The improvements to the Metro treatment plant have resulted in significant reductions in ammonia and phosphorus loads to Onondaga Lake , and an associated steep decline in the concentrations of these nutrients in the lake water. Productivity has declined, algal biomass is reduced, and the lake currently exhibits mesotrophic conditions. The strong correlation between Metro TP load and lake response is illustrated in Figure 4-9. The loading calculations presented in this graph are based on water year (October 1- Sept 30), due to the relatively short residence time (flushing rate three to four times per year) of Onondaga Lake waters. The summer average conditions are therefore more strongly affected by more recent inflows.

Effluent total N has remained relatively constant as the total P has declined, resulting in a significant increase in the N:P ratio of Metro effluent as well as the N:P ratio of the lake’s upper waters (Figure 4-10). The N:P ratio of a lake’s upper waters indicates the relative availability of the two important nutrients to the algal community, and the extent to which primary production is limited by phosphorus. The increasing N:P ratio in Onondaga Lake evident in Figure 4-10 is consistent with increasing P limitation. When the N:P supply ratio declines below a critical value, in the range of 15:1 or lower, P is present in abundance relative to the stoichiometric needs of the algal cells, and N may become limiting (Hall et al. 2005). Once N is limiting, there is a selective advantage for certain species of cyanobacteria, which have the ability to fix atmospheric N, to flourish.

The transformation in the quality of Metro effluent has effected a fundamental change in the lake ecosystem. A reduced phosphorus supply has resulted in lower algal biomass, since phosphorus is now firmly established as the limiting nutrient for algal growth in Onondaga Lake. Reduced algal biomass results in less organic material to be decomposed in the lower waters, and a reduced demand on hypolimnetic oxygen resources. The result is a decrease in volume-days of anoxia and increased dissolved oxygen levels during fall mixing (Figure 4-11). The oxidation of ammonia to nitrate in Metro’s biological treatment system has resulted in a statistically significant increase in nitrate concentrations in the lake’s upper and lower waters. The increased nitrogen concentrations are also a consequence of the lower phosphorus loading. As phosphorus and algal productivity have declined, there is diminished uptake of all forms of nitrogen from the water column.

The presence of nitrate in the lower waters has affected the redox status of the lower waters, and modified the dynamics of sediment phosphorus release. As oxygen is depleted from the deep waters, nitrate serves as an alternate electron acceptor for the microorganisms actively decomposing organic material settling out of the photic zone. As long as nitrate is present, reduction of iron and manganese is prevented, and phosphorus bound to these minerals remains trapped in the lake sediments (Figure 4-12).

Comparing the 2009 results to those of previous years highlights the effect the increasing nitrate levels have had on the redox status of the lake’s hypolimnion, as reflected in the diminished accumulation of SRP in the lower waters during the summer period of thermal stratification.

Once iron and manganese are reduced, phosphorus is released to the overlying waters and the SRP concentrations in the hypolimnion increase. If the phosphorus released to the upper waters includes more than that represented by decomposition of algae from the current year, it may be considered as an internal load (recycle). An estimate of the mass of phosphorus released from the lake sediments during the stratified period each year indicates that there is a great deal of variability; some change may be a result of improving redox status of the hypolimnion. However, variations in algal production and the duration of stratification also affect the magnitude of the internal phosphorus recycling.

4.5 Seneca River

The ACJ includes provisions for monitoring and modeling the water quality conditions in the Seneca River as part of a regional approach to wastewater management. The Seneca River is included on New York State’s compendium of impaired waters, due to low dissolved oxygen concentrations during warm water and low flow conditions. The outlet of Onondaga Lake joins the Seneca River as it flows north to Lake Ontario; the chemistry of Onondaga Lake waters clearly affects water quality of the river in the vicinity of the outlet. As part of the annual AMP, water quality conditions are monitored at Buoy 316 in the Seneca River during summer low flow conditions (Figure 4-13); data are collected from other buoy locations to support the Three Rivers Water Quality Model. Results of the 2009 program are reported in the library.

Between June and October, 2009, water-quality recording devices (YSI sondes) were deployed at Buoys 316, 236 and 409 to measure in-situ dissolved oxygen, pH, salinity and temperature at 15-minute intervals. Two sondes are placed at each location, one in upper waters and one in lower waters. These locations document ambient water quality conditions upstream of the “state cut”, an area of prolific dreissenid mussels (Buoy 409), upstream of the Baldwinsville-Seneca Knolls WWTP outfall and outlet of Onondaga Lake (Buoy 316), and downstream of the lake outlet and Wetzel Rd WWTP outfall (Buoy 236).

In addition to the high-frequency sonde monitoring, three full water quality surveys were conducted in 2009 on July 9^th (discharge 3350 cfs), August 12^th (discharge 5090 cfs) and September 24^th (discharge 783 cfs). Three additional surveys were conducted only at Buoy 316 on July 30^th (discharge 733 cfs), August 27^th (discharge 830 cfs) and September 16^th (discharge 729 cfs). Note that all the discharge data are considered provisional as of the date of this report. Taken together, these data portray water quality conditions in the Seneca River in response to point source discharges, biological conditions and changes in quality of the outflow. The water quality data collected in 2009 during the three full river surveys were generally similar to data collected in previous years. The data measured during the individual surveys were reflective of the predominant processes occurring in the river at that time of the year, including flow conditions, dreissenid mussel activities, and inflow from Onondaga Lake and subsequent mixing.

The higher salinity of Onondaga Lake waters compared to the Seneca River affects stratification and mixing of the outflow. Particularly when flow and velocity in the Seneca River are low, the more saline, denser water entering from Onondaga Lake forms a discrete lower water layer that is detectable at nearby locations. The salinity data collected during the September 2009 survey, when the river flow was relatively low, indicated stratification occurred downstream of the Onondaga Lake outlet.  The high salinity concentration observed in the bottom water between Buoy-269 and Buoy-240 was likely a result of mixing with more saline and denser water entering from Onondaga Lake, as well as the localized groundwater discharge at the “deep hole” area. There was no stratification observed at Buoy-296 during the September 2009 survey, which indicated the lake water has little influence to Seneca River upstream of the Onondaga Lake outlet during that survey. 

The Onondaga Lake outlet is not the only factor affecting water quality of the Seneca River. In the early 1990s, the invasive dreissenid mussels (zebra and quagga mussels) began to colonize sections of the Seneca River as they migrated eastward from the Great Lakes through the NYS Barge Canal system. Proliferation of the mussels along the river bed has profoundly affected the cycling of nutrients and organic material, and, consequently, the quality of the river water. Respiration of the benthic organisms depletes dissolved oxygen, and the river water has become notably clearer as phytoplankton and other particles are filtered out. Greater light penetration has allowed macrophyte growth to expand.

Results of the Seneca River monitoring program support an evaluation of compliance with ambient water quality standards and the development, verification and validation phases of the integrated TRWQM and OLWQM modeling initiatives. Validation of the lake and river models is underway using AMP data from 2004 – 2007.

The average river flows during the summer of 2009 were comparable to long-term average summer conditions, and did not approach low flows. Compared with the previous two years, the 2009 summer flow conditions were more variable, with flows ranging between 2,000 and 6,000 cfs. There were some periods at the beginning of August and during September when river flows declined; however, these periods were of relatively short duration. The average summer flow rate in 2009 was approximately 1,600 cfs, comparable to the long-term summer average of 1,700 cfs. As a reference, the seven-day average low flow condition for the Seneca River at the Baldwinsville monitoring site with a probability of recurring once in 10 years (the 7Q10 flow) is approximately 350 cfs. This figure is based on 55 years of record.

In 2009, there were just two individual days with flows falling below the 7Q10 threshold; water quality sampling did not occur on either day. Most significant to water quality and habitat conditions, 2009 streamflow was sufficient to prevent prolonged periods of low DO. As a result, the spatial trends of water quality parameters during the July and August surveys were similar in top and bottom waters and were overall less pronounced than those typically observed under lower flow conditions. Spatial trends observed during the September survey indicated stratified flow conditions and were consistent with trends observed during low flow surveys conducted in previous years. Notably, the water quality conditions in 2009 exhibited an improvement with respect to regulatory compliance as compared to conditions measured during 2007 with a comparable flow regime.

5. Biology and Food Web: 2009 Results and Trends

This section of the annual report reviews the extensive data describing the phytoplankton, macrophyte, zooplankton, dreissenid mussel and fish communities that comprise the Onondaga Lake food web. As phosphorus concentrations in Onondaga Lake have declined to mesotrophic levels, biological conditions have responded. Improved light penetration, a consequence of lower algal abundance, has led to expansion of macrophyte beds in the littoral zone; the macrophytes provide improved habitat and shelter for fish and other aquatic organisms. The decline in alewife abundance, which dominated the fish community between 2003 and 2006, has led to increasing diversity in the fish community.

5.1 Phytoplankton

Although phytoplankton abundance in 2009 was higher than measured in 2008, the average algal biomass for April-October remained well below that expected for a meso-eutrophic lake (3-5 mg/L, Wetzel 2001) and is similar to that of 2007, at 1.2 mg/L (Figure 5-1). Peak algal biomass did not exceed 3.5 mg/L in 2009, confirming the lake’s mesotrophic status. Over the last decade, phytoplankton biomass has declined significantly, and 2007, 2008 and 2009 were the three lowest years on record. This decline is likely due both to the improved removal of phosphorus from the Metro effluent and to increased grazing by dreissenid mussels.

Diatoms continued to dominate the phytoplankton community, but the seasonal pattern of succession of phytoplankton taxa was different in 2009 from that of 2008. In 2009, as in 2008, there was a spring bloom of diatoms, ending in mid-June. Unlike 2008, however, algal biomass, led by diatoms and dinoflagellates, showed a sharp peak of abundance in July (Figure 5-2 and Figure 5-3). A minor algal bloom (peak chlorophyll-a concentration less than 10 ug/L) in October and November of 2009 was dominated by chrysophytes; this taxonomic group was not an important component of the phytoplankton community in the fall of 2008.

The pattern of phytoplankton abundance in 2009 reflects food web dynamics, especially the interactions of alewife and zooplankton. The alewife population was down in 2009, which effectively released larger zooplankters, including Daphnia mendotae, from predation by this fish. In response, relatively large zooplankton were abundant. However, after a brief clear-water phase in late June 2009, the daphnids were eventually replaced by smaller Bosmina longirostris, a species that is far less effective grazing on the phytoplankton. This allowed the midsummer resurgence of a phytoplankton community dominated by diatoms, which was not evident in 2008. The decline of diatoms in late July and early August 2009 may have been caused by silica depletion. The hard, porous cell wall of diatoms is made almost entirely of silica, and diatom abundance can be limited by the availability of this element. The alternating peaks and valleys of silica concentration and diatom abundance seen in 2009 (Figure 5-4) support this interpretation. As in 2008, a bloom of diatoms appears in the late fall, perhaps enabled by the return of silica to the upper waters with lake turnover. A non-native species of diatom not previously recorded in Onondaga Lake (Actinocyclus normanii), was the most abundant phytoplankton species in 2009 and dominated the fall diatom bloom. Although this diatom likely originated in the marine and estuarine environment off the coast of Norway and Germany and in the Baltic Sea, it has successfully adapted to life in fresh waters, particularly those with an abundant nutrient supply (USGS Nonindigenous Aquatic Species Fact Sheet http://nas.er.usgs.gov/queries/FactSheet.aspx?speciesID=1695). This taxon is considered to be an invading species in the Laurentian Great Lakes (Mills et al. 1993), likely arriving in Lake Ontario in 1938 in ballast water, based on analysis of sediment cores. Actinocyclus normanii is also documented present in Lake Michigan, Lake Erie, and Lake Huron, and has been reported in Lake Superior. The Onondaga Lake phytoplankton historical data document that the spring diatom bloom has been typical of spring conditions, and that the silica concentrations in the upper waters are depleted as the bloom develops. However, until recently, diatoms did not exhibit the secondary peak in abundance in the fall.

Cyanobacteria and dinoflagellates, which dominated the phytoplankton community in Onondaga Lake until 2001, have now nearly disappeared from the lake, and nuisance blooms of Aphanizomenon (A. gracile and A. flos-aquae), typical of summers before 2000, no longer occur. The species of cyanobacteria remaining in the lake are smaller in size, and peak Cyanobacteria abundance reached only 0.03 mg/L in 2009.

5.2 Macrophytes

The macrophyte community continued its expansion within the lake’s littoral zone in 2009. Based on annual aerial photographs, coverage has expanded from 85 acres in 2000 to 382 acres in 2009. Extensive surveys are conducted every five years (2000, 2005 and 2010) to complete a species list and document changes in biomass. The AMP team completes limited field surveys of the macrophyte community the week of the aerial flights; this field program is used to verify the estimates of relative abundance and assess the species composition. In 2009, the most abundant species were submersed macrophytes (Table 5-1).

Table 5-1. 2009 Macrophyte Field Survey Results.
	Where Present		Overall
Species	Percent of Sites	Relative Abundance	Relative Abundance
Coontail (Ceratophyllum demersum)	90%	30%	27%
Common water weed (Elodea canadensis)	90%	28%	25%
Eurasian water milfoil (Myriophyllum spicatum)	80%	18%	15%
Southern naiad (Najas quadalupensis)	60%	23%	14%
Water stargrass (Zosterella dubia)	50%	40%	20%
Curly leaf pondweed (Potamogeton crispus)	40%	<1%	<1%
Small pondweed (Potamogeton pusillus)	10%	<1%	<1%

5.3 Zooplankton

The zooplankton community is a pivotal component of the lake ecosystem; these grazing aquatic animals affect the abundance and species composition of the phytoplankton community, and are, in turn affected by the fish community. The size structure and abundance of the Onondaga Lake zooplankton community is tracked annually as part of the AMP. In Onondaga Lake, the zooplankton and benthic mussels are the most important grazers of phytoplankton; larger zooplankton are far more efficient grazers and the presence of larger organisms results in less algae and clearer waters. The size structure of the zooplankton community, i.e., the relative abundance of small and large species, is a consequence of the grazing pressure exerted on zooplankton by fish.

The average biomass of all zooplankton in the lake (as measured in dry weight) was slightly lower during April-October 2009 (236 µg/L) than it was for the same period in 2008. The peak zooplankton biomass, evident in mid-June 2009, was 740 µg/L. During this period of peak abundance, the zooplankton community was dominated by taxa in the family Bosminidae, which are small crustacean species.

The average size of zooplankters from April to October 2009 (0.43 mm) was larger than during the years 2003-2005 (0.32-0.34 mm), years of peak abundance of alewives (Alosa pseudoharengus), the dominant fish planktivore (Figure 5-7). In 2009, as in 2008, larger species of Daphnia make up a significant part of the zooplankton community (Figure 5-5). The resurgence of daphnids (Figure 5-6) and the large average size of zooplankters in the summer of 2008 and 2009 (Figure 5-8) reflect the decline in alewife abundance in these years. However, the zooplankton data from 2009 suggest that the alewife population may be rebounding in the lake. In 2009, the average size of the zooplankton community decreased again in August (Figure 5-8). This decline is most likely a result of a strong year class of alewife and gizzard shad, and the associated high rates of predation on the larger zooplankton. Overall, the size structure of the Onondaga Lake zooplankton community is consistent with relatively high levels of herbivory by the fish community. According to Dr. Edward Mills, a member of the Onondaga Lake Technical Advisory Committee, the dominance of Daphnia mendotae in the zooplankton community suggests that zooplanktivory is reasonably intense in Onondaga Lake and that fish species like gizzard shad and white perch, in addition to alewife, may have an impact. The ultimate indication of low zooplanktivory in Onondaga Lake would be dominance of the very large Daphnia pulicaria.

5.4 Zebra and quagga mussels

The density of dreissenid mussels declined slightly in 2009, although the biomass increased (Figure 5-9), reflecting a shift in dominance from smaller zebra mussels (Dreissena polymorpha) to larger quagga mussels (Dreissena bugensis) (Figure 5-10). Since mussels are known to act together with lowered nutrient loading to keep phytoplankton biomass low (Idrisi et al. 2001, Zhu et al. 2006), water clarity in Onondaga Lake should continue to increase with continued reductions in phosphorus loading and continued expansion of the dreissenid mussels.

5.5 Fish

Changes in the fish community of Onondaga Lake are anticipated as water quality and habitat conditions improve. The significant reduction in ammonia and phosphorus input, and the consequent shift from eutrophic to mesotrophic conditions are expected to expand available fish habitat within both the littoral zone and the pelagic zone. Since 2000, the AMP has included an extensive fisheries monitoring program, incorporating different types of sampling gear to assess nesting, larval, juvenile and adult stages of numerous species. The challenge in data analysis and interpretation lies with the multitude of abiotic and biotic factors affecting the fish community, including weather and climate, interactions among species, food web effects and invasive species. This expanded discussion of the lake’s fish community is based on an analysis of the first decade of the AMP, a time of significant water quality changes. A technical appendix provides additional detail. The species identified in Onondaga Lake in 2009 are listed in Table 5-2.

Table 5-2. List of Fish Species Identified in Onondaga Lake, 2009.
Alewife	Brown bullhead	Golden shiner	Quillback	Walleye
Banded killifish	Carp	Largemouth bass	Rock bass	White perch
Black bullhead	Chain pickerel	Longnose gar	Shorthead redhorse	White sucker
Black crappie	Channel catfish	Northern hog sucker	Silver redhorse	Yellow bullhead
Bluegill	Freshwater drum	Northern pike	Smallmouth bass	Yellow perch
Bowfin	Gizzard shad	Pumpkinseed	Tesselated darter

Richness and Diversity

Several important metrics of the fish community are based on measured diversity and richness of the adult fish community, both littoral (near-shore) and pelagic (open water). Richness is a count of the number of species within a community, while diversity considers both the number of species present and their relative abundance. In Onondaga Lake, richness has generally increased over the decade of AMP monitoring, from 24 species in 2000 to 28 species in 2009. The lake is an open system, with easy migration into and from connected waterways through the Seneca River system. Over the last decade, some 45 fish species have been documented in the lake, comparable to regional waters.

Diversity of the fish community fluctuates in response to the periodic peaks and crashes of two species of clupeid, the alewife (Alosa pseudoharengus) and gizzard shad (Dorosoma cepedianum). Abundance of these two species of the herring family is highly variable, as Onondaga Lake is near the northern edge of their range, and both species periodically exhibit significant winter mortality. Extremes in recruitment are seen as well; both species periodically produce very strong year classes that dominate the catch for years, as individual fish can live 10 years or longer.

Reproductive Success

An assessment of fish reproduction is conducted by several methods including nesting surveys, sampling of larval fish, and sampling of young of year (YOY) fish. Evaluation of the young fish provides information on overall health of the fish community within the lake and success of reproductive efforts from year to year. Factors other than water quality, including water temperature during and after spawning, water levels, and trophic dynamics, can affect reproductive success and need to be considered.

The centrarchid species in the lake (largemouth and smallmouth bass, pumpkinseed and bluegill sunfish, rock bass) and bullhead construct nests in the littoral zone. Each year, the AMP team conducts nesting surveys to estimate the number and spatial distribution of the nests. In 2009, 1,995 nests were observed, with a fairly even distribution between the north (54%) and south (46%) basins. This represents a more even distribution; for example, as recently as 2007, 84% of the nests were located in the northern basin. More than half of the nests supported pumpkinseed sunfish.

The 2009 sampling program collected larval stages of alewife, bluegill, gizzard shad, pumpkinseed, white perch, and yellow perch in Onondaga Lake, documenting successful reproduction of these species. In addition, the 2009 field effort captured young-of-year (YOY) smallmouth and largemouth bass, brown and yellow bullhead, common carp, golden shiner, rock bass, shorthead redhorse, tessellated darter and white sucker. Larval samples were dominated by the alewife, indicating another strong year class for this clupeid species. Both the diversity and richness of YOY have increased over the decade of Onondaga County biological monitoring, indicating more species reproducing as well as a more balanced community.

Recreational Fishery

Onondaga Lake supports a varied recreational fishery, with largemouth bass, smallmouth bass, bluegill and pumpkinseed (Lepomis or sunfish species), yellow perch and brown bullhead some of the more common sport fish present. Population characteristics of these species were investigated to assess changes in the quality of the sport fishery. Specifically, the relative abundance of fish in various size classes available to anglers was evaluated along with general condition with regard to weight of fish of each species across a range of size classes. Angler diaries summarize catch rates for largemouth and smallmouth bass by anglers over time and compare rates to other waters.

Analysis of largemouth bass catch data indicates the size distribution of this species is skewed notably toward fish 8-15 inches (203-381 mm) in length, providing anglers with a consistently large proportion (~70%) of catchable-size largemouth bass of small to moderate length and a more variable proportion of fish of relatively large size. Fish exceeding 20 inches (508 mm) have been collected infrequently during AMP sampling efforts. This suggests that fish of this size are rare in Onondaga Lake or are not susceptible to capture by the sampling gear used. Analysis of largemouth bass weight by size class indicates that fish are relatively heavy for their length; suggesting that forage is not limiting.

In contrast, smallmouth bass in Onondaga Lake are not as heavy relative to their length as are largemouth bass.  The Wr values for smallmouth are <100, but they are not unusually low compared with regional lakes.  The lower relative weight likely reflects more limited forage for smallmouth bass (either due to competition or limited production of preferred forage).  The preferred forage of adult smallmouth bass is crayfish; these benthic crustaceans are not abundant in Onondaga Lake.

Size distribution of smallmouth bass in the catch has shown a distinctly different pattern than that of largemouth bass and indicates that recent catches are dominated by fish of small size (less than 11 inches). Since 2007, fish less than 11 inches have comprised approximately 90% of collected smallmouth bass; fish of this size comprised only 33-60% of the smallmouth bass in 2000-2004. The increase in the proportion of smaller smallmouth bass collected is due in part to an overall increase in the numbers of fish of this size, but also reflects declining numbers in larger size categories. However, this increase is considered to be a sampling artifact arising from a habitat shift. Improving water-quality conditions in the lake’s pelagic zone has made such areas more habitable for smallmouth bass. Larger smallmouth bass may also have shifted their habitat use to off-shore areas due to increased water clarity, increased vegetative cover in the littoral zone, and to take advantage of the abundant alewife as a forage base. Smallmouth bass occupying deeper, offshore habitats would be relatively unsusceptible to capture by the AMP sampling methods.

The analysis of sunfish catch indicates that the population is dominated by fish of 3-8 inches in length. Catch results suggest that sunfish production was poor in 2004 and 2005 but has increased since then, with relatively high numbers of fish of 3-8 inches available to anglers in 2008 and 2009. The poor production of bluegill and pumpkinseed in 2004 and 2005 may have been due to alewife predation on sunfish larvae. Alewife abundance has declined since 2005, which may have allowed for the recent production of stronger sunfish year classes.

Sunfish greater than 8 inches in the catch have been scarce; several factors may be contributing. It is possible that larger sunfish are not being captured in proportion to their abundance by the gear being used. Larger adult sunfish – at least bluegill - tend to be more pelagic than juveniles and smaller adults and may be captured disproportionately less than these other groups when electrofishing littoral habitats. Slow growth of fish after reaching reproductive age may also be contributing to low abundance of larger sunfish in Onondaga Lake. Weight analysis of adult-size fish indicates that forage is not limiting for sunfish in Onondaga Lake and energy reserves of individual fish are relatively high, so it is possible that this energy is being put into reproductive effort rather than body growth. Despite the scarcity of sunfish greater 8 inches, sunfish up to that size are readily available to anglers and are increasing in abundance in recent years.

Size distribution of yellow perch in the catch indicates that the population is dominated by fish 5-10 inches long. There have been occasional increases in the proportion of fish 10-12 inches long. From an angling perspective, the yellow perch fishery of Onondaga Lake is somewhat cyclic in nature due to fluctuations in year class success. The overall abundance of yellow perch has been increasing, and number of fish longer than 10 inches is also increasing. This translates to more and larger yellow perch available to anglers.

Analysis of the size distribution of the brown bullhead catch indicates that a relatively high proportion of catchable-size fish greater than 9 inches long, with just over 50% of catchable-size fish greater than 12 inches in 2009. This affords anglers an opportunity to catch relatively large brown bullhead. Overall numbers of brown bullhead have been increasing in recent years, suggesting that a high-quality brown bullhead fishery is becoming established in Onondaga Lake. Analysis of brown bullhead weight for various size classes indicated that brown bullhead in Onondaga Lake are in generally good condition, but not particularly heavy for their length.

Abnormalities

The occurrence of physical abnormalities in fish captured during AMP sampling is monitored using a standardized protocol known as DELTFM. DELTFM abnormalities are defined as Deformities, Erosions, Lesions, Tumors, Fungus, and/or Malignancies. Data are used for trend analysis and to compare fish collected from Onondaga Lake to those collected in other areas. Fish abnormalities can result from chemical contamination; biological agents such as bacteria, viruses or fungi; or interactions among multiple stressors. DELTFM abnormalities have increased in recent years. DELTFM abnormalities were found in 1.6% or less of adult fish from Onondaga Lake from 2000 to 2004, increased to 3.2% in 2005, decreased slightly to 2.6% in 2006, and then increased steadily to 5.1% in 2009 (Figure 5-11). The overall increase appears to be primarily related to increases in deformities (including injuries) and lesions (likely bacterial, fungal, or viral infections).

The species contributing the most to the DELTFM total in 2009 were brown bullhead (48% of total), white sucker (12%), gizzard shad (9%), pumpkinseed (8%), and largemouth bass (7%). Of the fish species found with abnormalities, the percentage of adults collected with DELTFM abnormalities was greatest for those species generally considered benthic or bottom-oriented. These species include brown bullhead, white sucker, shorthead redhorse, silver redhorse, channel catfish and bowfin.

Most of the abnormalities in the lake’s fish community in 2009 were lesions (63%), followed by erosions and deformities (15% each). Tumors, malignancies, and fungal infections were relatively rare (<6% combined). Brown bullhead has consistently had the highest incidence of DELTFM abnormalities of any species collected from Onondaga Lake.

The cause of the overall increase in DELTFM abnormalities since 2003 is not understood. No individual species that have consistently exhibited DELTFM abnormalities have shown a similar increase over time. Some of the observed overall increase is due to increases in the abundance of individual species over time. As an example, brown bullhead have been steadily increasing in abundance in the fish community as a whole. Because this species has a relatively high incidence of DELTFM abnormalities, an increase in the population size of brown bullhead has resulted in an increase in the total number of DELTFM abnormalities observed overall. This reasoning explains a portion of the observed increase, but it does not account for all of it.

The percent of fish of a given species with DELTFM abnormalities is highly variable from year to year; as a consequence, no individual species has demonstrated a statistically significant increasing trend in DELTFM abnormalities. Notable increases in lake-wide DELTFM abnormalities have occurred in 2005, 2008, and 2009. In each of these years, different species have shown marked increases in DELTFM abnormalities from the previous year. In 2009, one such species was gizzard shad. DELTFM abnormalities were found on 24% (21 of 88) of gizzard shad collected in 2009, compared to a previous high of 0.8% (1 of 123) in 2006. Similarly, the number of pumpkinseed with DELTFM abnormalities increased from a high of 5 in 2008 (3.9% of all abnormalities) to 18 in 2009 (8.0% of all abnormalities). A large increase in the incidence of DELTFM abnormalities in a species one year may be followed by a similar decrease the following year. The inconsistent and sometimes widely fluctuating incidence of DELTFM abnormalities in individual fish species complicates identification of causes of the apparent increase in DELTFM abnormalities over time in the lake.

The types of DELTFM abnormalities affecting fish in Onondaga Lake has changed over the course of the AMP. The incidence of deformities and tumors has declined considerably, while the incidence of lesions has increased significantly. Many factors can influence the incidence of lesions, including types and abundance of various bacteria and other pathogens in the lake, physical stress on fish (such as spawning activity, elevated water temperature, extremes in water chemistry), chemical exposure, and injury or stress from fish sampling programs and angling. Further study of the types of injury or infection associated with observed lesions is required to better understand what causes the observed lesions, why the incidence of lesions is increasing, and whether the causes are consistent across species.

The incidence of lesions and tumors in brown bullhead in Onondaga Lake from 2000 to 2009 was compared with similar data from waters in the Chesapeake Bay watershed, Great Lakes, and Cape Cod area. Prior to 2007, occurrences of lesions and tumors in Onondaga Lake brown bullhead were within the range associated with reference sites (typically <5% incidence) from this larger regional set of waters. Data since 2007 indicate a shift in occurrence to levels associated with contaminated sites from regional waters. The cause of this shift is not known, but as indicated previously, several pathogens affecting brown bullhead in Onondaga Lake have recently been identified. The incidence of lesions and tumors in brown bullhead in Onondaga Lake declined in 2009, reflecting an apparent recovery (at least partially) of the population from these pathogens. Another possible explanation for the observed increase in DELTFM abnormalities in recent years is that as water quality has improved over time, more of the lake area has become inhabitable for fish. As a consequence, benthic fish may be expanding their use of areas with contaminated sediments. Increased exposure to contaminated sediment could be causing an increase in DELTFM abnormalities in benthic species.

6. 6. Integrated Assessment of the Food Web

The improvement in the trophic status of Onondaga Lake over the last decade, following upgrades to the Metro wastewater treatment facility, is remarkable. From eutrophic conditions throughout the 20^th century, with frequent blooms of nuisance cyanobacteria and episodes of upper water anoxia, Onondaga Lake has now reached a state of mesotrophy similar to many other lakes of this region without histories of pollution. Algal blooms have diminished and water clarity has improved. Rooted aquatic plants have returned to the littoral zone, providing expanded nearshore habitat for fish and other aquatic animals. In addition, the improved water clarity, coupled with improved oxygen conditions throughout the summer, has created expanded habitat for fish species in pelagic areas.

Furthermore, the long-term monitoring required by the ACJ has allowed scientists to document the details of this transition and to integrate the importance of food-web dynamics. At first glance, the story seems simple: nutrient loading from Metro has been greatly curtailed, and excessive biological production in the lake has declined as a consequence. But the story is more complex, as events not directly related to this “bottom-up” effect have interacted in a synergistic manner to affect the biological community of Onondaga Lake.

The major decrease (more than 90%) in ammonia loading from Metro allowed two keystone species to expand successfully in the lake--the alewife and zebra mussels. A “keystone species” is one that exerts a large influence on the structure of an ecological community, despite its relatively small abundance. Both alewife and zebra mussels have had a major impact on food web dynamics in Onondaga Lake. The invasion of the lake by dreissenid mussels (zebra and quagga mussels)—important grazers on phytoplankton—has acted together with decreased nutrient loading to reduce phytoplankton abundance. Meanwhile, the explosion of alewives in the lake between 2003 and 2007 also led to “top-down” changes in the food chain, but of opposite effect, as these voracious grazers on the zooplankton released the phytoplankton from their consumers and led to increased algal production. The decrease in alewife abundance in 2008 and 2009 has allowed the return of larger species of zooplankton and had subsequent effects on the structure of the phytoplankton community. These changes have reverberated through the lake’s entire food web, including the rest of the fish community.

Alewife, while exerting strong predation pressure on zooplankton (as well as on pelagic larval fish), also serve as prey for larger fish. The presence of this pelagic prey, in conjunction with improved quality of the deep water, increased macrophyte abundance in the littoral zone, and improved water clarity may have contributed to a shift by larger smallmouth bass and yellow perch toward a more pelagic habitat. These food-web effects on water clarity are illustrated in Figure 6-1.

Not all of the effects of improved water quality may be beneficial to the fish community. Expansion of areas used by bottom-dwelling species may be a cause of increased DELTFM abnormalities as these species increase use of areas with contaminated sediments. This could explain the increasing incidence of DELTFM abnormalities in recent years.

Macrophyte coverage and abundance in Onondaga Lake has been increasing in response to water-quality improvements, particularly those resulting in increased water clarity. This has had significant ramifications for the fish community. Several fish species often associated with aquatic macrophytes during one or more life-history stages have shown significant increases in abundance. Most of these species are dependent on macroinvertebrate forage as juveniles and adults or prey on forage fish dependent on vegetated habitats. Some of these species also use aquatic macrophytes as a primary spawning substrate.

In years of high alewife abundance, fish with pelagic larvae (such as pumpkinseed, bluegill, yellow perch and white perch) have shown reduced recruitment, which is likely due to predation of larvae by alewife when alewife abundance is relatively high. Alewives, in turn, serve as forage for larger, fish-eating species, including smallmouth and largemouth bass, yellow perch, white perch and walleye. Changes in the size distribution of smallmouth bass - in particular since 2000 - suggest that larger adults of this species may have shifted to deeper, offshore habitat from shallower, littoral habitat. The availability of alewife as forage in pelagic habitats may be facilitating this shift. If such a shift has occurred, this would reflect a change in adult smallmouth bass foraging from a littoral-based food web to a pelagic-based food web.

Increased macrophyte abundance presumably has resulted in a substantial increase in production of macroinvertebrates in the littoral zone. This in turn promotes the observed increase in abundance of several littoral fish species that use macrophyte beds for foraging areas. These would include largemouth bass, pumpkinseed, yellow perch, and brown bullhead among others. Young-of-the-year sport fish and forage fish species, such as golden shiner, that prefer vegetated habitats are increasing in number as a result of expanded habitat. These small fish, in turn, provide additional forage for larger fish-eating species such as largemouth bass.

The proliferation of zebra and quagga mussels in the lake after reductions in ammonia levels may be helping to support the increased abundance of species like pumpkinseed by providing an abundant food source. Other species like freshwater drum, yellow perch and common carp that are known to feed on mussels are also likely benefitting from the increasing abundance of these mussels. Consumption of mussels by multiple fish species provides another connection between the littoral-based food web and the pelagic-based food web. The increasing complexity of the overall food web in Onondaga Lake is an important sign that the lake is recovering from past environmental perturbations.

Overall, there has been an increase in the quantity and quality of habitat available to fish species in Onondaga Lake. This has resulted in a slight increase in fish species richness with a more even distribution of fish throughout the lake. Many fish species, particularly those associated with vegetated habitats, are also increasing in abundance. The aquatic food web within the lake continues to diversify, with more species becoming more interrelated. This increasing complexity with regard to energy sources and energy flow results in an ecosystem that may be more resilient to environmental stress. The 2009 AMP findings indicate that this is an ongoing process and that more changes are likely to occur. As water quality continues to improve, and more diverse and higher quality habitats become established, further increases in aquatic species diversity, abundance and interrelatedness are expected.

7. Progress with Related Initiatives

Onondaga Lake is the focus of several on-going initiatives in addition to the major improvements to the wastewater collection and treatment infrastructure. The Onondaga Lake Partnership (OLP) was created in 1999 to coordinate the environmental revitalization, conservation, and management of Onondaga Lake. Members of the OLP are drawn from six agencies, the U.S. Army Corps of Engineers, Environmental Protection Agency, NYSDEC, the NYS Attorney General’s Office, Onondaga County, and the City of Syracuse. Other community groups and volunteers participate through two standing committees. The OLP website www.onlakepartners.org summarizes ongoing efforts.

Honeywell International, Inc., is proceeding with remediation of legacy industrial pollution under regulatory oversight. To date, efforts have focused on identification and removal of sources to prevent additional contamination from reaching the lake. Now, the remedial project effort is addressing contaminated lake sediments. Plans for sediment dredging and capping in certain areas, mostly in the southern littoral zone, are under review. Information on the Honeywell project submittals is available online at www.dec.ny.gov/chemical/37558.html on the NYSDEC website.

The Onondaga Lake Basin Model will be used to analyze the effects that proposed BMPs in the tributary subwatersheds are likely to have on the loads of phosphorus and nitrogen entering the lake. These BMPs will include both actions on the landscape (for example, guiding land use changes) and actions to manage hydrology (for example, through detention and storage). The link to reports of the Onondaga Lake Basin Model is http://ny.cf.er.usgs.gov/nyprojectsearch/projects/2457-AF3-1.html.

Onondaga County Department of Water Environment Protection and the Onondaga Environmental Institute (OEI) www.onondagaenvironmentalinstitute.org are collaborating on an extensive monitoring and surveillance program designed to identify and, ultimately, remediate dry weather sources of bacteria to the lower reaches of Onondaga Creek and Harbor Brook. Two phases of the investigation have now been completed, with multiple rounds of sampling during dry weather. Samples were collected from seven sites along a five mile segment of Harbor Brook, and 22 sites along a 24-mile segment of Onondaga Creek. Results have pinpointed specific areas where bacteria are entering the creeks, and helped direct remedial work on the aging wastewater collection infrastructure within the City of Syracuse.

A conceptual design and plan for revitalization of Onondaga Creek has been developed by representatives of the City of Syracuse, Onondaga Environmental Institute, Cornell Cooperative Extension of Onondaga County, Atlantic States Legal Foundation, the SUNY College of Environmental Science and Forestry, and Canopy, a coalition of parks associations and community gardens in the City of Syracuse. Project information is posted at www.esf.edu/onondagacreek/project.htm.

Each year, Onondaga County DWEP updates a bibliography of published information on Onondaga Lake. The engineering improvements to the wastewater collection and treatment infrastructure continue to be the subject of professional and trade publications and presentations. In addition, scientists and academics continue to analyze this unique case study of rehabilitation of a once-degraded lake. The human health impacts and ecological analysis of the contaminant issues are also analyzed by academic and agency scientists, public policy specialists, economists, and engineers. An annual Onondaga Lake Symposium is convened each November by the Upstate Freshwater Institute to discuss recent findings http://www.upstatefreshwater.org/html/annual_olsf.html.

Exploration of green technology solutions to the challenges facing Onondaga Lake is underway from multiple perspectives. In addition to investigating green solutions to urban storm runoff, the OLP is exploring alternative green technologies for mitigating the Tully Valley mudboils, a source of sedimentation to Onondaga Creek. Onondaga County’s “Save the Rain” initiative is an effort to educate the watershed community on effective measures to reduce runoff from the urban landscape. Information on porous pavement, tree planting, rain gardens, rain barrels and more are available at http://www.ongov.net/savetherain/index.html.

As efforts continue to reduce point and nonpoint sources of pollution to the lake, other projects are underway to enhance recreational access and opportunities for community involvement with the lake and its shoreline. Planning and design of Phase 1 of the Creekwalk to connect Onondaga Lake to Armory Square are complete and construction has begun. Phase 2 of the Creekwalk, connecting Armory Square to Kirk Park, is under construction

8. 8. Emerging Issues and Recommendations

From its inception, the Ambient Monitoring Program was designed for modification in response to new information or changes in regulatory policy. The fourth stipulation amending the ACJ directed Onondaga County to, among other actions, enhance the tributary component of the AMP; the program modifications will begin in 2011. A major objective of the enhanced program will be to evaluate the effectiveness of the green and gray infrastructure improvements. The enhanced tributary monitoring will likely include some testing of CSO-affected streams during storms for the presence and concentration of priority pollutants, such as heavy metals, pesticides and other organic compounds. The County will also review its tributary monitoring efforts to determine whether additional sampling during storms, especially during the summer, is warranted. In addition, a review of the potential benefits and costs associated with bacterial source tracking is recommended to help identify the source or sources of elevated fecal coliform bacteria, notable in lower Harbor Brook and Ninemile Creek. The Microbial Trackdown Study, which was undertaken as a joint project of the Onondaga Environmental Institute and OCDWEP, has provided a better understanding of dry weather discharges into Harbor Brook and Onondaga Creek.  Additional follow-up sampling and investigation has been recommended to monitor bacteria levels in the streams to gain a greater understanding of the spatial and temporal dynamics.

This 2009 AMP report includes an examination of the first ten years of data from the County’s fishery monitoring program. A few minor modifications to the fishery program design are recommended to address emerging issues and gaps. First, the significance of observed abnormalities on captured fish merits additional investigation and documentation. Several research and monitoring efforts to characterize the fish community are currently underway on behalf of Honeywell International and the State University of NY College of Environmental Science and Forestry. Noting likely capture injuries, such as erosion of a dorsal fin, may help differentiate potential impacts of exposure to sediment contaminants. Common carp are currently not examined for DELTFM abnormalities, due to the difficulty of examining these large fish on board the monitoring boat. As benthic feeders, the condition of carp in the lake may provide useful information, and it is recommended that a few (2-4) carp be examined in each of the electrofishing transects. Second, the County’s design for gill netting (short duration daytime net sets, parallel to shore) is not optimal; nighttime sets perpendicular to the shore would likely provide better capture. A side-by-side program is recommended to extend the utility of the historical data. Third, determining the age of fish captured would help quantify growth patterns. Onondaga County fisheries biologists have archived fish scales that could be aged; it is recommended that this effort proceed.

In addition to these relatively detailed recommendations related to the fisheries program, there is an important emerging issue that will affect analysis and interpretation of all the lake’s biological and habitat data. An extensive habitat restoration program will be implemented by Honeywell International, beginning in 2012, to mitigate the impact of legacy pollution and habitat loss. The plans call for dredging and capping some littoral areas, including regions of Onondaga Lake monitored for macrophytes, macroinvertebrates and fish as part of the AMP. Baseline characterization of affected areas is underway by consultants to Honeywell International. The County anticipates integrating the Honeywell activities and data into the overall evaluation of the lake’s ecosystem.

As water quality conditions of Onondaga Lake improve and become comparable to conditions measured in other waterways, non-indigenous species of zooplankton, mussels, phytoplankton, fish and macrophytes are able to become established. Invasive species from the Great Lakes basin are able to reach the lake through the Seneca/Oneida/Oswego Basin. Analysis of the status of non-indigenous aquatic species will be included in the 2010 AMP report; results of the 2010 intensive surveys of the macrophyte and littoral macroinvertebrate communities will inform this analysis.

The Onondaga Lake Water Quality Model is nearing completion. This important tool was developed and calibrated using data from the AMP, and has been subject to outside expert peer review. This model will serve the entire community by defining the water quality and aquatic habitat benefits, if any, realized by further reducing nutrient and sediment inputs from point and nonpoint sources.

9. Literature Cited

Callinan, C. E. 2001. Water Quality of the Finger Lakes. NYSDEC, Albany NY. 147 pp.

Carlson, R.E. 1997. A trophic state index for lakes. Limnology and Oceanography. 22:361-369.

Codd, G.A. 1995. Cyanobacterial toxins: Occurrence, properties and biological significance. Water Sci. Technol. 32(4):149-156.

Hall, S.R, V. H. Smith, D.A. Lytle and M.A. Leibold. 2005. Constraints on primary producer N:P stoichiometry along N:P supply ratio gradients. Ecology. 86(7):1894-1904.

Idrisi, N., E.L. Mills, L. G. Rudstam and D.J. Stewart. 2001. Impact of zebra mussels (Dreissena polymorpha) on the pelagic lower trophic levels of Oneida Lake, New York. Can. J. Fish. Aquat. Sci. 58(7): 1430–1441

Kishbaugh, S.A. 2009. NY State Citizens Statewide Lake Assessment Program (CSLAP): Interpretive Summary: Cazenovia Lake 2008.

Mills, E. L., J. H. Leach, J. T. Carlton, and C. L. Secor. 1993. Exotic species in the Great Lakes: a history of biotic crises and anthropogenic introductions. Journal of Great Lakes Research 19(1):1-54.  

Wetzel R. G. 2001. Limnology, Lake and River Ecosystems. Third Edition. Academic Press NY

Zhu, B., D.G. Fitzgerald, C. M. Mayer, L.G. Rudstam and E.L. Mills. 2006. Alteration of ecosystem function by zebra mussels in Oneida Lake: Impacts on submerged macrophytes. Ecosystems 9(6): 1017-1028.