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.