THE STATE OF LONG ISLAND'S BAYS

Long Island's bays were once famous for their clear waters, vast underwater eelgrass meadows and abundant shellfish harvests. Today, they are more likely to be murky and closed to shellfishing. The decline in water quality is being driven by increased nitrogen pollution from decades of expanded development without the proper wastewater and stormwater infrastructure. Last springs closure of shellfish harvesting in western Shinnecock and Quantuck bays due to Red Tide is just the latest chapter in an ongoing saga of harmful algal blooms plaguing our bays.

A MESS A G E FROM YOUR BAYKEEPER

Nutrient pollution (nitrogen and phosphorus) is the leading cause of water quality impairments in the U.S. Sewage wastewater discharges have been identified as the major cause of water pollution along one-third of Americas shorelines. Recent trends indicate that our local waters are in trouble. In 2006, New York State classified the western tributaries feeding Moriches Bay as Impaired Waters (303d), a listing reserved for the most degraded and threatened waterbodies. In 2010, Great South, Moriches, Quantuck and Shinnecock bays were placed on the list due to reoccurring Brown Tide blooms attributed to excess nitrogen loadings from onsite sewage disposal systems and runoff. Lake Agawam, Old Town Pond and Mill Pond were listed for failure to meet dissolved oxygen standards. Although the specific causes are undetermined, low dissolved oxygen levels are most often attributed to excess nutrient loadings. Although recent data suggests some positive developments in the fight against pollution and habitat degradation - hard clams and scallop populations are improving, fluke stocks are nearly rebuilt and porgies have surpassed target goals - steep challenges remain ahead. The ill effects from the current approach to wastewater management have reached the tipping point. Our commercial and recreational fishing interests, real estate values, tourism and the use and enjoyment of our maritime environment all depend on clean water. Clean water should be a right, not a privilege. If we let our local waters continue to degrade, we have no one to blame but ourselves. The time to act must not be delayed.

Red Tide in Great Peconic Bay

C RE ATI NG THE REP ORT

"Baywatch 2011: The State of Long Island's Bays is based on the best available information about indicators representing three major categories - habitat, fisheries and pollution - in the Peconic and South Shore estuaries. These watersheds have distinct differences, so some indicators may be specific to one area or the other. Wherever possible, Peconic Baykeeper accessed the most recent data to build on information presented in "Baywatch 2008." In all instances, information from government agencies, independent scientists, and other environmental organizations were used to analyze trends. Peconic Baykeeper arrived at environmental-quality ratings by measuring current findings against those recorded in the 1970s, when scientifically derived baselines for many indicators first became available. The condition of the bays is further described in upward or downward trends; the arrow up (positive), sideways (neutral), or down (negative) next to the letter grade indicates the effect that the efforts of public or private agencies have had on particular indicators of bay health. When confronting limits and gaps in available information, Peconic Baykeeper used its best judgment to determine the ratings.

A = Excellent B C F
= Good

s s t

Improved Outlook Little or No Response Declining Outlook

= Marginal

D = Poor
= Failing

H AB ITAT H EA LT H
EELGRASS HO P E TA KES R O O T Ds
Eelgrass beds provide shelter while serving as both spawning and nursing grounds. They also improve water clarity by dampening wave energy, stabilizing sediment, producing oxygen, and sequestering nutrients to lower the level of nitrogen and phosphorus in the water. Declines in local bay scallop populations are closely correlated to the eelgrass crash. Long Island's once vast eelgrass meadows have suffered dramatic declines making restoration efforts essential. Monitoring throughout the Peconic Estuary shows most sites suffering 100% losses. But there is some encouraging news as scientists from Cornell Cooperative Extension, working on healthy meadows at both Cedar and Orient points, have seen shoot density increases. They hope to plant multiple acres of eelgrass at several sites within Suffolk County in the near future. Eelgrass Density in the Peconic Estuary
Bullhead Bay Gardiners Bay Northwest Harbor Orient Point Southold Bay Three Mile Harbor Cedar Point Orient Point

900
Eelgrass Density (shoots/m2)

800 700 600 500 400 300 200 100 0 1996

1998 2000 2002 2004 2006 2008 2010

DIADROMOuS FISH HABITAT CLIMBING THE LADDER

Freshwater tributaries flowing into the South Shore and Peconic estuaries allow diadromous fish to migrate between freshwater and marine environments, often for spawning. Unfortunately, many passages are obstructed by dams, culverts, etc. Long Island is home to a number of diadromous fish, including alewives, American eels, river herring and sea-run trout. Restoration efforts have been ongoing to remedy obstructions to diadromous fish habitats and the South Shore Estuary is now home to our first permanent fish passage - a fish ladder in Carmans River. Another fish ladder has been established in Massapequa Creek. Several additional restoration efforts being planned could potentially reopen ten miles of habitat. Peconic tributaries have also seen progress. A fish passage recently completed at Peconic River's Grangeable Park reopened 24 acres of spawning ground and 1.5 miles of tributary water with

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Photo by Tom Schlichter

The newly completed Grangeable Park fish ladder

up to 50,000 alewives passing through this spring alone. More work is planned for Peconic River and its tributaries. By improving our current knowledge of alewife populations through continued monitoring, we can better develop and evaluate restoration efforts.

SEA LEvEL THE TIDE IS RISING

Ct
loss. With higher levels, habitats will also be lost to inundation. Sea level rise will increase the depth of water over eelgrass beds, reducing available light levels. It will also lead to flooding and inundation with some areas submerged on a regular basis or even permanently. Climate change is also expected to cause more frequent and severe storms, intensifying flooding and altering sediment transport while modifying structure of tidal wetlands and beaches. It is difficult to determine the response of estuarine habitats to sea level rise as much depends on the changes (size and depth) to the bays. Certainly, sea level rise will accelerate coastal erosion, resulting in the potential loss of beaches and bluffs while encouraging shoreline hardening. Barrier islands will face the greatest impacts. At higher projections, storm surges might flow across the islands, creating new inlets and altering adjacent estuarine communities. A rise in sea level will also result in the water table rising. This will submerge septic systems in some areas, possibly releasing untreated human waste pollutants to coastal waters. A higher water table will also saturate terrestrial lands, leading to increased runoff. Freshwater systems will experience saltwater intrusion, with saltwater pushing further inland and altering established ecosystems by shifting vegetation and impacting anadromous fish. Freshwater habitats may try to migrate inland but will likely be rebuffed by structural barriers.

By 2020s LOw END 2-5" HIGH END 5-10"

By 2050s 7-12" 19-29"

By 2080s 12-23" 41-55"

Projected Levels of Sea Level Rise for Long Island

Climate change is a global issue with potentially local impact. When water temperature increases water also increases in volume, a phenomenon known as thermal expansion. Because the volume of the oceans increases while the size of ocean basins remains unchanged, sea level rises. The melting of polar ice caps may also contribute to sea level rise. Each aquatic ecosystem provides a valuable function that will be fundamentally changed by sea level rise. At the low estimates, tidal wetlands and the intertidal areas may migrate inland when possible. Shoreline hardening will prevent some of these migrations, resulting in species
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F IS H ER I E S
BAY SCALLOPS A NUMBERS GAME Cs
Bay scallops are renowned for their delicately sweet flavor and for once being a vibrant local fishery. They spawn only once during their two-year life spans and are highly vulnerable to environmental changes. Brown Tide and loss of eelgrass, in addition to overharvesting, have contributed to the collapse of this fishery. Since Brown Tide first appeared in the Peconic Estuary back in 1985, bay scallops have been severely depleted. Landings have hovered between 2,000 and 4,000 pounds for two decades and, despite the absence of Brown Tide since 1995, it is possible too few scallops remain to drive a full-scale natural recovery. Still, landings have been on the rise since 2007 with upwards of 18,000 pounds harvested in 2009. This may indicate some recovery of the population. Improvements in restoration techniques, replanting of eelgrass and the absence of Brown Tide in the Peconics have contributed to the uptick in harvest numbers.
Scallop Landings
20 18 16 14 12 10 8 6 4 2 0
Peconic Bay Estuary South Shore Estuary

Landings in 1,000s lbs

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009

HARD CLAMS REASON FOR HOPE

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Hard clams improve water quality through filter feeding. At the height of the Long Island fishery in the 1970s, abundant clams filtered 40% of Great South Bay. Today, they filter merely 1%. With the demise of bay scallops in the Peconic Estuary, fishing pressure shifted to hard clams resulting in severe decline. In 2008, Senator Chuck Schumer declared the fishery a disaster. That same year, hard clam dockside value was only $600 thousand compared to $12 million at the fisherys peak. After steadying for a few years at approximately 20,000 bushels, landings rebounded to more than 80,000 bushels in 2010, indicating a possible comeback thanks to restoration efforts supported by the South Shore towns, Suffolk County and The Nature Conservancy.
Hard Clam Landings
100 90 80 70 60 50 40 30 20 10 0
Peconic Bay Estuary South Shore Estuary

Landings in 1,000s of Bushels

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
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FINFISH HIT AND MISS

C+ s
35 30

The Department of Environmental Conservation (DEC) monitors Peconic Estuary finfish populations through tow surveys, recording 87 different species over the past 25 years. A number of these fish represent key commercial and recreational fisheries. Some are forage fish - prey for larger predatory fish - and an important link in the marine food web. Many also use these estuarine waters as spawning and nursery grounds. The strong connection between finfish and their environment makes the health of fish populations a good indicator of the condition of our estuaries. Not all of the news on the finfish front is bad. Scup (porgy), whose Mid-Atlantic stock was deemed overfished in 2006, is considered rebuilt with a biomass up to 130% of the target set by management agencies. Bluefish have slowly recovered from low numbers in the 1970s and our regional stock has been rebuilt since 2009. The summer flounder (fluke) stock is not quite rebuilt but spawning stock is at 89% of the target and rebuilt status may be achieved by 2013 if projections hold true. This is a significant improvement from fluke stocks being overfished in 2006. Of course, there are still points of concern. Many species, although not technically overfished, show signs of stress. Changes in predation, competition and/or environment have increased natural mortality for weakfish. Atlantic menhaden are troubled by low recruitment, and numbers of spawning class butterfish are at an all-time low. Outlooks for Atlantic herring and northern puffer are uncertain while windowpane flounder are overfished. Tautog (blackfish) are vulnerable to overfishing due to slow growth and reproduction plus a tendency to congregate around easily targeted structure such as rock piles. Winter flounder are of most concern. A favorite of anglers both recreational and commercial, the New England/Mid-Atlantic stock is at an all-time low with declines in reproductive adults and recruiting juveniles. Flounder are considered overfished with a 2008 stock assessment recording this species at only 9% of the biomass target. Because of its sensitivity to habitat degradation, winter flounder are especially vulnerable to local decline. Management efforts to rebuild winter flounder numbers revolve around reducing fishing mortality, particularly for the spawning stock. This requires a delicate balancing act with a mortality rate both sustainable for the flatties and sufficient for anglers. Management plans also call for minimization of habitat degradation caused by pollution and dredging.
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Winter Flounder Abundance in the Peconic Estuary

In 1,000s

25 20 15 10 5
87 88 89 90 91 92 93 94 95 96 97 98 99 01 02 03 04 05 06 07 08 09 10

Year

Winter Founder on Moriches Bay

OTHER IMPORTANT COMMON SPECIES

Bay Anchovy weakfish ** winter Flounder *,** Northern Puffer * Tautog *,** Summer Flounder **,*** Bluefish **,*** Striped Bass ** Herring
* Considered of concern by Department of Environmental Conservation ** Managed by Atlantic States Marine Fisheries Council *** Managed by Mid-Atlantic Fishery Management Council

87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09 10

200 180 160 140 120 100 80 60 40 20 0

Total Abundance of Fin sh in the Peconic Estuary

In 1,000s

Bay Anchovy

Scup

Fin sh

Photo by Tom Schlichter

P OL L uTI ON
NuTRIENTS A PLAGUE TO OUR WATERS Dt
Although a natural component of aquatic ecosystems, nitrogen in high concentrations can cause problems. Excess levels of nitrogen and phosphorus promote the growth of harmful algal blooms which consume oxygen, block light needed by other organisms and, in some cases, produce toxins. As Peconic Baykeeper boldly asserted in "Baywatch 2010: Nutrient Pollution, A Plague to Our Waters," changes in groundwater nitrogen are primarily driven by population growth. Excess nitrogen is delivered to Long Islands estuaries through residential cesspool leaching and sewage treatment plant effluent, fertilizers and agricultural runoff, atmospheric deposition of polluted air and discharge from boats. A study by Kinney and Valiela found the primary source of nitrogen loading to the South Shore Estuary to be wastewater from septic systems that have leached into the groundwater. The recently released groundwater study (Comprehensive Water Resources Management Plan) commissioned by Suffolk County reveals that nitrogen levels in groundwater have increased dramatically in the Upper Glacial and Magothy aquifers between 1987 and 2005 (40% and 200% respectively). Thus, nitrogen loading has a greater impact in areas that are not sewered, such as Moriches and Shinnecock bays. In 2010, the DEC declared the entire South Shore Estuary as Impaired Waters citing Brown Tide and nitrogen loading as the cause. This area includes all of Suffolk Countys South Shore bays: Great South, Moriches, Quantuck and Shinnecock. Peconic Baykeeper has been out in front on this issue, leading the charge to enact proactive measures restricting the amount of nitrogen released into ground and surface waters. We strongly encourage formation of sub-watershed management plans that include establishments of Total Maximum Daily Load (TMDL) for waterbodies harmed by nitrogen overload.

HARMFuL ALGAL BLOOMS A CLOUDED FUTURE

Dt

Phytoplankton serve as the base of the water column food web. However, when numbers of these microscopic plants grow out of control, proliferated by elevated nutrient levels, they discolor the water resulting in Red or Brown Tide. These harmful algal blooms disrupt ecosystems by producing toxins, shading sea grasses and consuming oxygen. Brown Tide, caused by the microalga Aureococcus anophagefferens, first appeared in Long Island waters in 1985, decimating local bay scallop and eelgrass populations. The worst bloom thus far, with a peak density of 2 million cells per mL, occurred in Great South Bay in 2008, prompting Senator Chuck Schumer to declare a disaster for the hard clam fishery. Although Brown Tide has virtually disappeared from the Peconic Estuary (PE) in recent years, it still reoccurs annually in Quantuck and Shinnecock bays. Both areas have been included on the DEC's list of "Impaired Waters." Long Island waters have also been home to Red Tide. Blooms of Cochlodinium polykrikoides first appeared in 2004 in Flanders Bay and eventually spread to areas of Great Peconic Bay and Shinnecock Bay, where it now occurs annually. Cochlodinium is known to be lethal to finfish and harmful to shellfish. Another Red Tide species, Alexandrium fundyense, has been found in the Forge River and Quantuck Bay of the South Shore Estuary (SSE) and in Meetinghouse Creek of the Peconic Estuary. This bloom is the causative agent of paralytic shellfish poisoning.
Peak Harmful Algal Bloom Densities in SSE and PE 30
Brown Tide (100,000 cells/mL) (1,000 cells/mL)

25 20 15 10 5 0 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
7

Cochlodinium

Brown Tide

Cochlodinium

B A CTE R I A L CONTAMINATIO N B U G S I N THE WATER

Ds

Bacterial pathogens are a significant threat to our local waters. Often originating from stormwater runoff, particularly following heavy rains, they may also originate from residential septic system leaching and boat discharges. Elevated levels not only harm the ecosystem; they make the waters unsafe for recreational use and shellfishing. Through the summer months, a number of beaches are closed to bathing by Suffolk Countys Department of Health Services due to elevated levels of pathogens. The county continually advises 24-hour emergency closure of more than 60 beaches because of the potential levels of bacteria following heavy rain events. The DEC also monitors for high levels of bacterial pathogens, specifically relating to the safety of shellfish consumption. Although this problem is not getting worse, it is still persistent and shows no signs of abating. Government agencies have taken measures to reduce bacterial pollutants including reducing runoff, establishing management plans for stormwater that include the development of Total Maximum Daily Loads (TMDLs) for bacterial contamination, and designating "no discharge zones" for boating, which Peconic Baykeeper has been instrumental in establishing.

Peconic Baykeeper is a membersupported environmental organization dedicated to defending Long Island's coastal waters. Through science-based monitoring, public education and legal initiatives, Peconic Baykeeper is working to restore our bays to their traditional role in Long Island life - a source of pleasure and prosperity for all.

SOuTH SHORE ESTuARY Total Acres Closed 32,901 34,084 36,284 35,664 % Acres Closed 29.7 30.8 32.8 32.2

PECONIC ESTuARY Total Acres Closed 5,765 6,239 6,048 6,055 % Acres Closed 3.6 3.9 3.8 3.8

For more information and to become a member, please contact: Phone 631.653.4804 Fax 631.653.4802 web www.peconicbaykeeper.org Email info@peconicbaykeeper.org Office P.O. Box 893 Quogue, New York 11959

YEAR 2007 2008 2009 2010

Special thanks to
mediaThe foundation, inc., Long Island Community Foundation and Mr. John de Cuevas for providing the funding that made possible the production of Baywatch 2011.