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Water: Estuaries and Coastal Watersheds

Challenges and Approaches

Introduction to Common Estuarine Environmental Problems

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Although each of the estuaries in the National Estuary Program (NEP) is unique, they all face the following nine environmental challenges: (1) alteration of natural hydrologic flows, (2) aquatic nuisance species, (3) climate change, (4) declines in fish and wildlife populations, (5) habitat loss and degradation, (6) nutrient loads, (7) pathogens, (8) stormwater, and (9) toxics.The challenges were identified by EPA staff and the Association of National Estuary Programs (ANEP) with input from NEP Directors and staff, scientists, outreach coordinators, citizens, business representatives, and local government officials.

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In general, these problems cause declines in water quality, living resources, and overall estuarine ecosystem health.More specifically, they all have significant economic, ecosystem, and socio-economic impacts; for example, local governments close shellfish beds when water-borne pathogens in shellfish tissue threaten human health; over-enrichment of nutrients in the water column causes dissolved oxygen levels to decline; the waters become "dead zones" where fish cannot survive. The introduction of aquatic nuisance species can adversely impact native species populations and their habitats.

The NEPs exchange information among themselves and with other coastal watershed managers about their approaches to successfully addressing these challenges.That exchange is critical to the effective restoration and protection of estuarine health across all the NEPs. The following describes each common challenge and depicts sample approaches that several NEPs have taken to address the challenges.

For more information about these common challenges, see the National Water Quality Assessments (305(b) Report).

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Alteration of Natural Hydrologic Flows

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As people alter the environment through activities like development, construction of dams, flood control structures, and diversions of water, we change the volume and rate that water runs off the landscape, into the ground, and into streams.Increased runoff can result in erosion and sedimentation.Changes in freshwater inflows to estuaries can adversely affect shellfish survival, and fish reproduction and distribution.

NEP Approach

Barataria-Terrebonne National Estuary Program

Hydrologic modifications to the Mississippi River for flood control have dramatically reduced freshwater flows in the Barataria-Terrebonne estuary.This has contributed to wetland losses and saltwater intrusion.The Davis Pond Diversion structure on the Mississippi River upstream of New Orleans is currently the largest Mississippi River diversion into the Barataria Basin and it is operated to send freshwater, nutrients, and small amounts of sediment into the Barataria system.The diversion is used as a means to control salinity and enhance vegetation.The Barataria-Terrebonne National Estuary Program represents local stakeholders on the Davis Pond Advisory Committee which authorizes and directs the operation of the structure.The advisory committee is currently re-evaluating the Davis Pond operational plan so that the diversion can be operated to enhance a greater area of wetlands in the lower Barataria Basin without adversely impacting estuarine-dependent species.

Morro Bay National Estuary Program

While estuaries naturally fill as part of the geologic process, this process has been accelerated as much as ten times the natural rate in Morro Bay, due largely to changes caused by people. Fires, overgrazing, erosion from development and loss of floodplains all contribute to increased sedimentation in the estuary.It is estimated that the estuary could lose all of its open-water and inter-tidal habitat within 300 to 400 years.

Increased sediment also causes impacts to plants and animals. Increased sediment in the water can bury or block sunlight from reaching eelgrass beds, destroying these underwater meadows.Sediment also buries and clogs gravel spawning beds for steelhead trout.

The Morro Bay Estuary Program and its partners take a holistic approach to restore the natural sedimentation process by (1) stopping sediment at the source and (2) catching it downstream before it reaches the estuary.To stop sediment at the source, a fire management plan was developed to help local fire districts reduce the risk of large catastrophic fires that leave bare slopes vulnerable to erosion.The Program, local Resource Conservation District and ranchers work to improve grazing practices and to fence cattle out of creeks, further reducing erosion.To date, approximately 35% of stream miles in the watershed have been fenced from cattle.The Program has also partnered with land owners to improve constantly eroding ranch roads. For example, Camp San Luis Obispo road improvements funded partially through the Program will prevent an estimated 2,800 cubic yards of soil from entering the nearby creek.

Ranch road erosion - photo credit: Morro Bay NEP

Photo Credit: Morro Bay NEP

The Program and its partners also work to restore the expansive historic floodplains diminished by past agriculture practices.One such project, the Chorro Creek Enhancement Project, is estimated to have prevented over 150,000 cubic yards of sediment from reaching the bay. To date, approximately 300 acres of historic riparian floodplain have been protected or restored.These floodplains not only trap sediment from reaching the bay, but also provide important fish and wildlife habitat. Currently, through the Program's monitoring efforts, staff are working to create accurate annual sediment loading values for the tributaries in the watershed.This data will help the Program better target areas for project implementation and will also help refine the current Sediment TMDL in the watershed.

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Aquatic Nuisance Species

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As the ease of transporting organisms across the Americas and around the globe has increased, so has the rate of both intentional and accidental introduction of aquatic nuisance species (ANS).Those introductions have had unexpected ecosystem, economic, and social impacts. ANS harm native fish and wildlife in many ways. They can take over native species' habitat, out-compete and prey upon those species, and disturb entire food webs. They also have major impacts on human activites by: disrupting agriculture, shipping, water delivery, recreational and commercial fishing; undermining levees, docks and environmental restoration activities; impeding navigation and enjoyment of local and regional waterways.

NEP Approach

San Francisco Estuary Partnership

The San Francisco Bay is one of the most "invaded" estuaries in the world.The San Francisco Estuary Partnership (SFEP) has employed two approaches to minimize the impacts of ANS.The first approach has involved serving on advisory groups, coordinating meetings, conducting specific projects, and producing educational brochures. In particular, the SFEP worked with the State Coastal Conservancy, the California Department of Fish and Game, and other state and Federal agencies involved with invasive species to complete the State Aquatic Invasive Species Management Plan. The plan was approved by the Federal Aquatic Nuisance Species Task Force in November 2007 and signed by California's Governor in January 2008. The SFEP also has worked on the 100th Meridian Initiative, a collaboration among state and Federal agencies, private industries, and citizens working to prevent the westward spread of zebra mussels through education and outreach by encouraging such measures as voluntary boat checks. This partnership includes the six states that straddle the 100th Meridian (100º longitude), the Canadian province of Manitoba, and most of the western states.

SFEP also supported efforts aimed at controlling the spread of the Chinese mitten crab.Mitten crabs were first introduced elsewhere in the U.S., but they became the first established U.S. population after being introduced into San Francisco Bay.Once established, the crabs excavate and burrow into river banks, eroding those banks and damaging levees. The crab's sharp claws also cut through commercial fishing nets and reduce or damage catch. The mitten crab can host a human parasite known as the lung fluke, which causes tuberculosis-like symptoms (note: this parasite has not been found in California crabs to date).At Federal and state fish salvage facilities associated with the California Aqueduct and State Water Project, the crabs clogged screens, holding tanks, and transport trucks used to salvage fish from the pumping stations.To mitigate the crabs' impact on those fish salvage efforts, the state built "Crabzilla", an 18-foot high traveling fish screen at one facility.In the fall of 1998, the state collected and transported approximately one million mitten crabs trapped by the screen, transporting them to another facility that ground them up for fertilizer.By 2005, the mitten crab population in the San Francisco Bay watershed had declined considerably. To learm more, view the invasive plan for San Francisco Bay Exit EPA Disclaimer.

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Climate Change

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Estuaries will face unique impacts from climate change.Many coastal wetlands and other estuarine habitats are threatened by inundation and erosion as the rate of sea-level rise accelerates. Climate change will also increase stresses to habitat and fish and wildlife populations as temperatures rise.Water quality problems are likely to worsen in estuarine waters if more extreme precipitation events create increased polluted runoff.

NEP Approach

Charlotte Harbor National Estuary Program

The Climate Ready Estuaries (CRE) Program helps coastal managers assess climate change vulnerabilities and develop and implement adaptation strategies, engage stakeholders, and share lessons learned.The 25 - 100-year planning horizon for climate change impacts seems to pose too great a challenge for many local decision makers.Officials in Punta Gorda, Florida, however, embraced the opportunity to work with the Charlotte Harbor National Estuary Program (CHNEP) to develop a climate change adaptation plan, and are already working to incorporate adaptation measures into strategic planning goals.CHNEP held public workshops and worked as a facilitator of the city's adaptation planning process, which identified the city's overall climate change vulnerabilities, as well as the mitigation strategies and adaptation techniques that could be used to address them.A process for the city to implement identified actions was also developed.The adaptation plan is serving as a sourcebook of ideas to make the city more resilient.The assessment of Regional climate change vulnerabilities and the planning model was adopted by the city of Punta Gorda, which has subsequently served as a model for Lee County's adaptation planning (Punta Gorda is located in Lee County).These communities have taken on the complex long-range challenge of climate change with plans that provide a basis for incremental actions that can make a significant difference in the long run, but do not have huge costs today.Punta Gorda's Plan includes a total of prioritized acceptable and unacceptable adaptation options as defined through group consensus. The plan underwent public, city staff, and council review before it was unanimously accepted in November 2009.Punta Gorda's comprehensive plan now explicitly indicates which areas will retain natural shorelines and constrain locations for certain high-risk infrastructure.The community has the data and analysis, as well as a framework to consider the menu of adaptation options that make sense at any point in time.

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Declines in Fish & Wildlife Populations

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The many stresses on estuaries have corresponding impacts on fish and wildlife.As their habitats disappear, the food they depend upon decreases and water quality degrades. Invasive species provide added pressures, replacing many of our native plants and animals.

NEP Approach

Sarasota Bay Estuary Program

In Sarasota Bay, historical maps and charts reveal that many once-vibrant oyster communities have disappeared.The SBEP selected for an oyster habitat enhancement project two sites that were physically disturbed and whose oyster communities were destroyed by coastal development during the 1960s.

This oyster habitat enhancement project builds on the success of an earlier pilot project in Sarasota Bay which demonstrated that prospective locations for building new oyster habitats were substrate limited.Oysters will not recover without the introduction of suitable and sufficient substrate material.The Sarasota Bay Estuary Program (SBEP) team created four and a half acres of oyster habitat at two locations in Sarasota Bay--two and a half acres at White Beach in Sarasota County and two acres at the Gladiola Fields in Manatee County.

map of Sarasota Bays

Both locations offered unique opportunities to create oyster habitat where none existed.White Beach is in a highly urbanized setting where oyster beds had once flourished but were then destroyed by shoreline alterations and residential development.The Gladiola Fields lie adjacent to suburban agricultural fields.Among other benefits of this project, creation and restoration of oyster habitat in these areas should result in improvements in local water quality by filtering urban stormwater runoff and nutrient-enriched drainage from agricultural fields.This restoration technique can be readily transferred to other Florida estuaries with similar oyster habitat structure that currently lack viable oyster populations.

Oyster habitat design for this project replicated existing oyster habitat in Sarasota Bay.At both sites, the SBEP built five, 75-foot diameter reefs utilizing fossil shell for the structural foundation. Each reef perimeter consists of a ring of oyster shell "sausages"— shell kept in biodegradable bags to prevent washout and dispersal. The reef interiors consist of loose shell thatprovides multi-dimensional, or 3-D, complexity. The fossil shell provides substrate for local oyster seed to attach onto and grow.The SBEP team monitors the reefs for oyster survival, growth, and utilization by fish and invertebrates.

Volunteers have contributed to every aspect of this project, helping to create the oyster "sausages", or bags of fossil oyster, transporting shell and unloading it onto the reefs, and assisting with basic reef monitoring.The following environmental and community groups provided over fifty volunteers and dedicated 400 hours toward all phases of this project: SBEP Bay Guardians, Sarasota Bay Parrot Head Club, University of South Florida Environmental SustainaBULLs, Friendship Volunteer Center's Retirees in Service to the Environment (RISE) Program, and Reef Innovations.

This project is funded in part through a national partnership grant between the NationalOceanic Atmospheric AdministrationCommunity-Based Restoration Program and The Nature Conservancy.

photo of a oyster shell covered shoreline photo of a cluster of oyster shells photo of two people pulling oyster shells out of the water photo of several people putting oyster shells onto a boat
All Photos by: Jay Leverone - SBEP

A significant challenge for oyster habitat restoration in Sarasota Bay and other coastal counties in Florida involves the permit process. To deploy material in Sarasota Bay, permits are required at the Federal (US Army Corps of Engineers), state (Department of Environmental Protection) and local (Sarasota County Environmental Permitting) levels.Even though those agencies' staff approved the two projects, a special exemption was required before the projects could be undertaken, as there is no standardized process for obtaining permits from all levels of government for sub-tidal habitat restoration.Several workshops in Florida have featured information about these projects in order to develop a strategy to address these permitting issues.

Another challenge is to ensure that oyster habitat project sites are adequately marked and proper signage is installed to prevent incidental navigation problems or accidents from boats travelling outside marked channels.SBEP has worked with staff from both counties to install and maintain appropriate markers.

Monitoring newly-created oyster reefs is appropriate for establishing the effectiveness of construction methods. It is also often required by permitting and funding agencies.For example, NOAA-funded projects must be monitored for two years.SBEP is currently monitoring both reefs for oyster recruitment, growth, and survival.Fish utilization of the constructed reefs will begin in October 2011.

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Habitat Loss and Degradation

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The health of marine and estuarine systems, and the human economies that depend on them, rely on high-quality habitats that provide essential food, cover, migratory corridors, and breeding/nursery areas for coastal and marine wildlife.For humans, healthy coastal habitats attract the tourism revenues and seafood industries that are vital to many localeconomies.These habitats also function to make coastal areas more resilient to storms and sea level rise.As coastal populations increased, coastal habitats have been converted due to development, highway construction, diking, dredging, filling, bulk heading, and other activities that degrade coastal ecosystems.

NEP Approach

Albemarle-Pamlico National Estuary Program

Submerged aquatic vegetation (SAV) produces dissolved oxygen that fish need to survive, filters pollution, and serves as a food source, hiding place, and home for fish, shellfish and crustaceans.SAV is valued at about $12,000 per acre per year because of its importance to overall aquatic health and fisheries.In North Carolina, SAV plays an important role in the state's $1.75 billion fishing industry, which employs 24,000 people.

In an effort to better protect North Carolina and Virginia coastal environments and the states' fishing industries, the Albemarle-Pamlico National Estuary Program (APNEP) led a state-Federal effort to develop a map of underwater fish habitat along the entire North Carolina and southern Virginia estuarine coastline.Project participants mapped 138,741 acres of SAV in the Albemarle-Pamlico estuary, which spans southeastern Virginia and northeastern North Carolina.The map provides for the first time baseline information about the location, quantity, and quality of underwater grasses along the coastline.This information helps planners take steps to avoid development impacts on vulnerable, valuable SAV acreage.The baseline map also enables scientists for the first time to assess changes in North Carolina and Virginia coastal waters' pollution levels over time and to learn how coastal conservation efforts are working.

To map the states' SAV, airplanes with special cameras flew 1,795 miles along the estuarine coastline during a two-year period. Wind, waves, high humidity and sediment-laden water from rainfall sometimes interfered with the ability to photograph the SAV, so volunteers sampled the water for clarity to ensure conditions were right for the high-altitude flights.Boat crews with underwater cameras also confirmed the accuracy of SAV locations.APNEP continues to work with state, Federal, university, and non-profit partners to establish an ongoing monitoring program for SAV through the North Carolina SAV Partnership. For more information, view the baseline map Exit EPA Disclaimer or check out the APNEP website Exit EPA Disclaimer.

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Nutrient Loads

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Nutrients such as nitrogen and phosphorus are necessary for growth of plants and animals and support a healthy aquatic ecosystem. In excess, however, nutrients can contribute to fish disease, red or brown tide, algae blooms, and low dissolved oxygen. Sources of nutrients include point and non-point sources such as sewage treatment plant discharges, stormwater runoff, faulty or leaking septic systems, sediment in urban runoff, animal wastes, atmospheric deposition originating from power plants or vehicles, and groundwater discharges.When excess nutrients lead to low dissolved oxygen levels, marine animals with little mobility can die; others must leave the hypoxic zones for more oxygenated waters.

NEP Approach

Long Island Sound Study

The Long Island Sound Study (LISS) identified the need to reduce nitrogen pollution and hypoxia as the highest priority for the Sound.Subsequently, LIS NEP developed and implemented a bi-state total maximum daily load (TMDL), which resulted in a landmark agreement between Connecticut, New York, and the EPA to reduce human sources of nitrogen by 58.5 percent. The LIS NEP's close partnership with the states of New York and Connecticut fostered an innovative TMDL approach that can serve as a model for how flexibility and market forces achieve efficient waste load allocations. The LIS NEP Management Plan called for reductions in point and nonpoint source nitrogen loading to the Sound to improve water quality and reduce hypoxia. The LIS NEP worked with the states and local governments to adopt aggressive nitrogen reduction targets and a nitrogen TMDL for the Sound. This TMDL establishes an enforceable schedule for point and nonpoint nitrogen reduction to the Sound over a 15-year period. The LIS NEP helped Connecticut develop a general permit to incorporate nitrogen load limits for participating publicly-owned treatment works in the watershed. The LIS NEP also fostered New York's bubble permit proposal for dischargers to the Sound. The Connecticut general permit scheme incorporates a nitrogen credit trading program that, in concert with the TMDL limits, sets a historic precedent in finding new ways of meeting water quality standards and protection while keeping costs down for taxpayers. In the first year of implementation, 39 plants reduced nitrogen output below their assigned permit limits, making them eligible to sell nitrogen credits valued at $2.76 million.

In 2010 the LIS NEP TMDL resulted in a reduction of 39,000 tons of nitrogen entering the Sound.The same year, the size of the hypoxic area decreased from 180 to 169 square miles and the duration of the hypoxia event decreased from 79 days to 45 days. The TMDL is posted on the LISS website. Exit EPA Disclaimer

Tampa Bay Estuary Program

Tampa Bay is Florida's largest open-water estuary, stretching 398 square miles at high tide.The Tampa Bay Estuary Program (TBEP) has focused on controlling nitrogen sources to restore vital underwater seagrass beds.Seagrasses are an important barometer of the Bay's health because they require relatively clean water to flourish. They also provide vital habitat for sportfish such as sea trout, snook, and redfish.The program set up the Tampa Bay Nitrogen Management Consortium, an innovative, public-private partnership, has developed an action plan to achieve nitrogen reduction goals.

Local governments, municipalities and private businesses around the country realize the importance of a healthy water environment to the economy of their regions.Many also face requirements to meet Federal, state and local water quality regulations through NPDES permits, TMDLs, and in Florida, numeric nutrient criteria.In Tampa Bay, local communities working with the Tampa Bay Nitrogen Management Consortium developed voluntary water quality goals and nutrient loading targets to support recovery of clear water and underwater seagrasses in the mid-1990s, and have collectively implemented more than 250 projects (resulting in 400 tons of nitrogen reduced) since 1996 to help meet the nutrient loading targets.

In 1998, the USEPA approved a regulatory Total Maximum Daily Load for Tampa Bay, and in 2007 stated that all permitted nutrient sources within the Tampa Bay watershed would be required to have an annual numeric limit, or allocation, for their nitrogen discharge to Tampa Bay.The Consortium (more than 45 local governments, businesses and agencies) decided to develop voluntary nitrogen limits for themselves and provide those limits as recommendations, rather than relying on the regulatory agencies to develop allocated numeric limits.EPA and the Florida Department of Environmental Protection (FDEP) participated in this effort throughout the process.Over a two-year period, Consortium members developed fair and equitable allocations for all 189 sources within the watershed.The FDEP has accepted the water quality-based effluent limits as meeting water quality requirements for Tampa Bay.

Consortium members have each contributed funds ($5,000 each) to support a technical contractor to work with them to develop scientifically-sound options for allocations.Consortium members realize that by combining their funds, the cost to each member is much reduced over what would be required for technical support individually.Consortium members have estimated that if one entity wished to fund technical support individually for their allocation, the cost to that entity would be more than $100,000.The Tampa Bay Estuary Program facilitates the Consortium, manages the technical support contractor, and collects the funds from Consortium members for contractor support.

Key benefits identified by the Consortium members include the fact that:allocations are equitable and based on sound science, the process and allocations were developed by Consortium participants (not regulatory agencies alone), and the collective process was cost-effective for all participants.

Efforts such as these have led to impressive progress toward Tampa Bay's long-term goal of recovering 12,350 acres of seagrasses Bay-wide.Tampa Bay gained 3,250 acres of seagrass between 2008 and 2010, an 11 percent increase that is the largest two-year expansion of seagrasses since scientists began regular surveys of this critical underwater habitat.The Bay now supports more seagrasses than at any time measured since the 1950s. Water is now meeting clarity goals and regulatory requirements, and seagrass has expanded by more than 8,000 acres since 1999.

Data on trends is collected by scientists with the Southwest Florida Water Management District's Surface Water Improvement and Management (SWIM) Program. They assess seagrass coverage in the Bay approximately every two years, using a combination of maps produced from aerial photographs followed by ground-truthing to verify accuracy. The aerial photographs are taken in winter months when the water is clearer. Results of this comprehensive effort have been used to track trends in seagrass extent in estuaries throughout Southwest Florida since 1988. All major Bay segments showed seagrass gains, according to the SWIM data, including the Old Tampa Bay segment in the northern part of the Bay, which has been plagued by algae blooms and an expanding layer of thick, soupy muck near Safety Harbor in recent years.Seagrasses in Old Tampa Bay expanded by 858 acres over 2008 levels, or nearly 15 percent. Seagrasses in Middle Tampa Bay increased by 1,549 acres, or 23 percent.The increases could be a result of improving water quality overall. Results from 2010 monitoring indicate that all Bay segments met TBEP's adopted water clarity goals. Recent low-rainfall years, with less runoff entering the Bay, may have contributed to the improvements. And some gains also may be a function of constantly improving seagrass mapping techniques. Despite the impressive gains, the Bay is still 5,103 acres short of the target goal for seagrass set by the Tampa Bay Estuary Program and its local government partners. "Reaching that goal will require a continued commitment by the region to reducing excess nitrogen which remains the Bay's primary pollutant of concern", said Holly Greening, Executive Director of the Estuary Program. Too much nitrogen fuels algae growth that turns the water cloudy and depletes oxygen. "The seagrass increases are great news, especially as we mark the 20-year anniversary of the Estuary Program partnership this year," Greening said. "But we still need to manage nitrogen loadings, and to assess and address problem areas in the Bay."

For more management approaches, view the March 1, 2010 Webcast Seminar: Managing Nutrients in the National Estuary Program. This webcast highlights how three NEP projects — Tampa Bay in Florida, Delaware Inland Bays in Delaware, and Peconic Bay in New York State — are addressing nutrient issues.

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Pathogens are disease-causing microorganisms such as viruses, bacteria, and parasites that can create health risks for people enjoying recreation in and on the water.Pathogens can be introduced into estuaries from inadequately treated sewage, runoff from urban areas and animal operations, medical waste, boat and marina waste, combined sewer overflows, and waste from pets and wildlife. They pose a health threat to swimmers, divers, and seafood consumers.

NEP Approach

The Santa Monica Bay Restoration Commission

For many years now, population growth and the uncontrolled development of land have had serious impacts on the water quality of Santa Monica Bay.Popular swimming beaches are often posted with warnings due to high pathogen levels found near storm drain outlets and tons of trash and pet waste are frequently washed from city streets into the Bay during storm events.Finding solutions to water quality impairments caused by pathogens requires an understanding of where the pollutants come from (sources), how they reach the Bay (pathways), and how they affect Bay resources (impacts).

The adverse impacts on water quality of pathogens from stormwater and urban runoff have been well documented.The Santa Monica Bay Restoration Commission conducted a landmark 1995 epidemiological study that provided, for the first time, indisputable scientific evidence linking health risks with swimming in urban runoff-contaminated waters.Although the sources of pollutants are numerous and disparate, pathogens are ultimately the product of all the people, as well as their pets, that live in the Bay's watershed.Pathogens are transmitted to the Bay via numerous pathways - runoff from lawns and streets into creeks and storm drains, municipal wastewater,commercial discharges, and boating and shipping activities, to name a few.Urban and stormwater runoff carried to the Bay through the region's massive storm drain systems is a serious, year-round concern. On average, 30 billion gallons of stormwater and urban runoff are discharged every year through more than 200 outlets; even in dry weather, ten to 25 million gallons of water flow through storm drains into Santa Monica Bay every day.Because the region's 5,000-mile network of storm drains was built to convey flood waters to the ocean as quickly as possible, all wet-weather flow and most dry-weather flow bypasses wastewater treatment facilities and discharges directly to the Bay.Reducing the level of pathogens to the Bay is one of the key goals of the Santa Monica Bay Restoration Plan, which emphasizes preventing pollution at the source and pollution reduction targeted to specific areas.

Stormwater and urban runoff are regulated through municipal, industrial, and construction National Pollutant Discharge Elimination System (NPDES) permits. Mandated by Congress under the Clean Water Act, the NPDES Stormwater Program is a comprehensive national program for addressing sources of stormwater discharges that adversely affect the quality of our waters. The Program uses NPDES permits to require the implementation of controls designed to reduce the level of harmful pathogens from being washed by stormwater runoff into local water bodies. Permit holders are required to develop and implement Stormwater Pollution Prevention Plans or Stormwater Management Programs using Best Management Practices (BMPs) to prevent the discharge of pollutants into the Bay.These efforts will improve the water quality of the Bay to ensure that the waters are swimmable and fishable, the ultimate goal of the Clean Water Act.

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Stormwater runoff is generated when precipitation from rain and snowmelt events moves across the landscape without percolating into the ground. As the runoff flows over the land or impervious surfaces (paved streets, parking lots, and building rooftops), it accumulates debris, chemicals, sediment or other pollutants that could adversely affect water quality if the runoff is discharged untreated.

NEP Approach

Buzzards Bay National Estuary Program

To assist communities in meeting their stormwater challenges, the Buzzards Bay NEP provided summer jobs for students interesting in learning GIS mapping techniques, and assisted them in surveying roadways and shorelines in the Buzzards Bay study area to map the existing stormwater infrastructure.This information was provided to Fire Departments to help them respond to hazardous material spills.The data was also used to create an Atlas of Stormwater Discharges in the Buzzards Bay Watershed. The Atlas and companion CD, which was distributed to municipal boards and local libraries, includes maps of more than 2,600 stormwater discharges and more than 12,000 catch basins along the shores of nearly all of Buzzards Bay.Boards receiving the document and poster size maps included Boards of Selectmen, Departments of Public Works, Boards of Health, and Conservation Commissions. The NEP also developed a set of "Unified" regulations to ensure consistency among Planning Boards, Conservation Commissions, and Boards of Health in addressing stormwater issues in their community.The principle behind these regulations was that no new construction should create any new direct untreated stormwater discharges that degrade water quality or living resources, and that stormwater must be treated onsite.A rainfall of 1-1/4 inches or greater occurs in the Buzzards Bay area on average every four months. The NEP adopted the standard of treating the first 1-1/4 inch rainfall on the impervious surface within a watershed. This rule captures, on average, 90 percent of the rainfall volume that falls in a given year. The program also offers technical assistance in implementing these stormwater regulations.

Casco Bay Estuary Partnership

The Casco Bay Estuary Partnership (CBEP) has been instrumental in advancing an innovative strategy to clean up stormwater pollution in areas developed before widespread use of effective stormwater management techniques.Long Creek is an urban stream near Portland, Maine that suffers from a variety of water quality problems. The Long Creek watershed is home to one of the largest retail and commercial centers in Maine (the Maine Mall).

Nearly one-third of the watershed is covered with impervious surfaces such as roads, parking lots, and rooftops. Stormwater runoff had been identified by the State Department of Environmental Protection as the source of the water quality problems, and the Conservation Law Foundation threatened legal action if problems were not addressed.Business and landowners in the watershed were faced with new legal obligations to clean up the Creek, which could have run to $10,000 per impervious acre per year.The Casco Bay Estuary Partnership played a central role in parlaying those new legal obligations into a voluntary, community-based, collaborative approach to the restoration of Long Creek. At the heart of the program is a sustainable funding mechanism through which private property owners address their permit obligations by collectively financing stormwater management throughout the watershed.

map of Long Creek Watershed

The 2000+ acre Long Creek Watershed, with the Maine Mall and associated commercial development to the lower right.

The Casco Bay NEP was instrumental in getting landowners to work together rather than separately.The collective approach, based on a 10-year, $14 million watershed restoration plan, allowed participants to target the most cost-effective projects first, defer less valuable projects, benefit from economies of scale, and qualify for low-interest State Revolving Fund (SRF) loans.The effect was to reduce costs to landowners by about two thirds.

The Long Creek Watershed Management District (LCWMD) is currently made up of owners of more than 115 properties within the watershed who have signed the "Participating Landowner Agreement," demonstrating that a collaborative approach to stormwater management can be attractive to the business community.

Already, the Long Creek Watershed Management District has installed more than $2 million worth of water quality improvement structures ("BMPs").An accelerated construction schedule was made possible by SRF funding, to be repaid over twenty years by fees paid by participating landowners.

A comprehensive stormwater BMP maintenance and inspection database has been constructed to assist LCWMD staff and landowners with upkeep. The first annual round of catch basin cleanouts and street sweeping has been completed.Landowners appreciated both the efficiency and quality of the program, while enjoying significant economies of scale. The Long Creek water quality monitoring program is the most comprehensive urban watershed monitoring effort in Maine, and among the most sophisticated in New England.

CBEP continues to be closely involved with efforts to improve water quality in the Long Creek watershed.CBEP Director Curtis Bohlen serves on the Board and as Treasurer of The Long Creek Watershed Management District (LCWMD). Bohlen has also taken a lead role in developing the water quality monitoring program and serves as an ad hoc member of the LCWMD Technical Committee. CBEP provides support for efforts in Long Creek in a variety of ways, including loaning water quality monitoring equipment, providing meeting space for LCWMD-related meetings and facilitating collaboration between LCWMD and area scientists.CBEP recently provided funding to analyze water samples collected in Long Creek to determine nitrogen concentrations.

Puget Sound NEP
Innovative Stormwater Management: Transitioning the Region to LID

Stormwater runoff causes many serious problems in Puget Sound – in fact, it may be the most serious undermanaged threat to the health and vitality of the Sound. Studies show that the source of many toxic chemicals found in the Sound are delivered via surface runoff. NOAA researchers document very high mortality rates of salmon within hours of entering urban streams — due to stormwater runoff. More and more of the Sound's productive shellfish rearing and harvest areas are closed due to stormwater runoff. High stormwater flows cause flooding and damage fish and wildlife habitat, contributing to iconic salmon species being threatened with extinction.

The Puget Sound NEP (Puget Sound Partnership) recognizes the limitations of conventional stormwater management techniques in protecting water resources from the many effects of stormwater runoff. That's why the Partnership, and its predecessors, have worked with regional partners since 2000 to transition the region to the use of low impact development (LID) practices. And it's happening – today the Puget Sound region's a hotbed of LID activity.


  • LID will soon be required in the region. Following appeals of the region's municipal stormwater NPDES permits, the Pollution Control Hearings Board ordered the Washington Department of Ecology to require LID where feasible in new permits. Ecology's draft municipal permits for the region contain LID requirements. See the 2012 Draft Municipal Stormwater General Permit Comment Period page for more information.
  • New technical assistance is available.
    • Cover of Integrating LID into Local Codes manual
    • To help local government staff integrate new LID requirements into their codes and standards, and as the next step in their LID Technical Assistance Program, the Partnership developed a new step-by-step guidebook, Integrating LID into Local Codes.
    • To ensure LID projects are properly sited, designed, built and maintained, the Partnership is again teaming up with Washington State University (WSU) Extension, Puyallup to revise the LID Technical Guidance Manual for Puget Sound.
  • Several local governments have LID programs – Seattle Public Utilities' "Green Stormwater Infrastructure" program continues to lead the way with award winning street redesign and redevelopment projects.
  • WSU and Stewardship Partners are leading a campaign to install 12,000 rain gardens in the Seattle/Puget Sound Region by 2016. The Join us in a rain garden campaign to protect Puget Sound! site contains a running total of how many have been installed. The program is gaining great popularity – it has been featured on the PBS Newshour.
  • WSU Puyallup has one of the most extensive LID testing and research centers in the nation. The center also offers state of the art professional training on key aspects of LID siting, design, installation and maintenance.

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Metals, such as mercury, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and pesticides enter waterways through storm drains; industrial discharges; runoff from lawns, streets, and farmlands; discharges from sewage treatment plants; and atmospheric deposition.If consumed by humans, organisms that are exposed to these toxics can pose a risk to human health. Wildlife and aquatic plants and animals can also be harmed by consuming contaminated fish and water.

NEP Approach

San Francisco Estuary Partnership

Outdoor insecticide applications—commonly used in California to control ants—have been directly linked to toxicity in California creeks.In 1998, all urban creeks in the San Francisco Bay Area were added to the Clean Water Act Section 303(d) list due to known or suspected impairment from the pesticide diazinon.This pesticide has since been "phased out" and has not been available for purchase since late 2004. Diazinon use is declining and is being replaced by other pesticides such as pyrethroids.Cleaning up indoors after using pesticides—and using pesticides indoors in ways that cause them to be washed down drains—has also been linked to water pollution, because sewage treatment plants are not designed to remove pesticides.

The SFEP's Urban Pesticide Pollution Prevention (UP3) Project Exit EPA Disclaimer works to prevent water pollution from urban pesticide use. The UP3 Project tracks, analyzes, and shares information about:(1) urban pesticide use, (2) regulatory processes related to pesticides of concern, and (3) science and monitoring data on pesticides. The UP3 Project supports the Urban Pesticides Committee, which for more than a decade has provided a forum for stakeholders to coordinate and develop ways to reduce pesticide impacts on aquatic life. The UP3 Project also provides tools to help municipalities reduce their pesticide use.This Project works to reduce this toxicity in creeks in three main ways:

  • Providing tools to municipalities to reduce municipal pesticide use and to conduct outreach to their communities on less-toxic methods of pest control (e.g., baits, caulking, and improved sanitation).
  • Compiling the latest relevant scientific information and providing regular e-mail updates and informative annual reports.
  • Providing technical assistance to California Water Boards and municipalities to promote the U.S. Environmental Protection Agency (U.S. EPA) and the California Department of Pesticide Regulation (DPR) support for preventing water quality problems from pesticides.

Specifically, the SFEP UP3 has:

  • Established the UP3 web site, which is cited by researchers, water quality managers, and regulators as a key resource for their work.
  • Trained hundreds of municipal staff and pest managers on the links between pesticide use and water quality and how to manage ant problems using integrated pest management.
  • Completed the only available analysis of urban pesticide use patterns (PDF) (14 pp, 231K,About PDF) Exit EPA Disclaimer to inform water quality and pesticide agency responses to pesticide-related surface water toxicity.

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