Managing Common Estuarine Environmental Problems

Introduction | Nutrient Overloading | Pathogens | Toxic Chemicals | Habitat Loss & Degradation |
Introduced Species | Alteration of Natural Flow Regimes | Declines in Fish & Wildlife Populations

See also Challenges Facing Our Estuaries.

Introduction

Each of the 28 National Estuary Programs (NEPs) are working to address their estuarine environmental problems through a combination of regulatory and nonregulatory programs as well as inclusive planning and management, scientific research and monitoring, innovative initiatives, and public outreach and education. The following discussion provides examples of how different NEPs around the country are tackling common environmental problems in order to protect and restore some of America's most significant bays, harbors, sounds, and lagoons.

To top of page

In Long Island Sound, USEPA and the States of New York and Connecticut, in partnership, are implementing a phased approach to reduce nitrogen loadings to Long Island Sound.

• Phase 1, announced in December 1990, committed the states to freeze point and nonpoint nitrogen loadings to the Sound in critical areas at 1990 levels.
• Phase 2, announced in the CCMP, goes beyond the freeze by committing to low cost actions to reduce the annual load of nitrogen below the 1990 freeze baseline.
• In 1998, Connecticut, New York, and the EPA reached a landmark agreement to reduce human sources of nitrogen by 58.5 percent by 2014.  A TMDL was developed and approved by EPA in 2001.

The greatest source of nitrogen in Connecticut and New York—about two-thirds—comes from the treated sewage discharged from sewage treatment plants. Since 1990, about 25 percent of the 105 treatment plants that discharge into the Sound and its tributaries in New York and Connecticut have completed full upgrades, known as biological nutrient removal. As a result of upgrades completed by the end of 2003, Soundwide discharges from plants have been reduced by 25 percent since the early 1990s.

Although progress has been made, nutrient overloading is causing hypoxic conditions in the western water of LIS every summer. Hypoxia is a condition of very low (or none at all!) oxygen in the water, these areas are often referred to "dead zones."

Dissolved Oxygen in Long Island Sound Bottom Waters Click here for a full view of this map.
Dissolved Oxygen	Severity of Impact
0.0 - 0.99 mg/L 1.0 - 1.99 mg/L 2.0 - 2.99 mg/L 3.0 - 3.49 mg/L 3.5 - 4.79 mg/L 4.8 + mg/L	Severe Moderaterly severe Moderate Marginal Interim management goal Excellent - Supportive of marine life
Map courtesy of the Connecticute Department of Environmental Protection and Long Island Sound Study

To top of page

A variety of management approaches are being undertaken by the National Estuary Programs. The following are some examples.

The Long Island Sound Study recommended that regional management of the major sources of pathogens continue and that site-specific management plans for embayments and shellfish bed areas be developed and implemented. Attention was directed to the following sources (in priority order): combined sewer overflows, nonpoint source runoff, sewage treatment plant malfunctions, and vessel discharges. Local watershed protection efforts are now being implemented.

The Peconic Estuary has focused on prevention of additional stormwater pollution and cost-effective stormwater mitigation efforts. Key elements of the plan include stormwater runoff mitigation from roadways, land use controls for new development, open marsh water management (improving hydrology and habitat at previously ditched marshes), the "no discharge zone" process (currently being coordinated in early stages), and best management practices (e.g., implementation of Coastal Zone Act Reauthorization Amendments Section 6217(g) management measures). Local governments, working with New York State, Suffolk County, and the Citizens Advisory Committee, are critical to this effort.

The New York-New Jersey Harbor Estuary Program has developed seven objectives to address pathogens: reduce loadings from CSOs, storm water discharges, and non-point sources; reduce or eliminate the discharge of raw or inadequately treated sewage due to sewage treatment plant malfunctions and illegal connections; establish marina pumpout facilities and no discharge zones to reduce impacts of vessel discharges; develop additional indicators of pathogenic contamination; continue interstate dialogue on beach closure policies to ensure a reasonably consistent approach; optimize disinfection practices; and continue appropriate research, environmental monitoring, and modeling to identify remediation activities and support recovery of uses.

The Corpus Christi Bay Program is considering the following actions: modification of existing monitoring programs; assessment of alternate/additional public health indicators for use in seafood monitoring and water quality; development of a coordinated database and networking system among public health professionals to facilitate exchange of information; and development of an information clearinghouse to address public fears and misinformation through outreach efforts.

In Santa Monica Bay, the implementation and financing of an epidemiological study was the result of a successful partnership between the State of California, local cities and agencies, Chevron Companies, private foundations, a local environmental group, and USEPA, working under the auspices of the NEP. As a result of study findings, the Program has recommended that federal and state agencies review and revise existing water quality Standards and Criteria for contact recreation in marine waters. A Beach Regulatory Protocol (that governs beach closures and public advisories about potential health risks) has been revised to include the posting of more strongly worded warning signs near flowing drains.

The Indian River Lagoon program is recommending the development and implementation of a program to inspect septic tanks on a periodic basis to ensure they are functioning properly and meet current design standards. A national demonstration project funded by USEPA in partnership with the Water Management Districts and local governments will provide additional information about impacts on the Lagoon and its resources.

In Sarasota Bay, Manatee County, Sarasota County, and the City of Sarasota have worked cooperatively to eliminate wastewater discharges and replace septic tanks with central sewers. Two state agencies, the City and County of Sarasota, and the Estuary Program have jointly conducted a study to detect the presence of human pathogens in surface waters.

The Casco Bay program is considering technical assistance to monitor and open public swimming areas and train installers and pumpers of septic systems, the adoption of minimum standards for stormwater quality in state and municipal regulatory programs, and requiring proof of legal waste disposal upon transfer of property.

In San Francisco, the Regional Water Quality Control Board and various municipal treatment plants are working together to raise the effluent limit for total coliform to still be protective of water quality while reducing the use of chlorine as a disinfectant. Chlorine is a dangerous chemical to handle and produces harmful by-products. All cities and sanitary districts are improving their operations and maintenance of systems to minimize leaks and spills. The Water Quality Control Board and various city and county urban stormwater agencies are working together to reduce nonpoint sources of pathogens. Richardson Bay has been designated a "No Discharge Area."

In N.C. (Albemarle-Pamlico Sound region), nonpoint source teams are being set up in each of the state's 17 major river basins. These teams will have representatives from agriculture, urban stormwater, construction, mining, on-site wastewater disposal, forestry, solid waste, wetlands, groundwater, natural resource agencies, local governments, special interest groups, and citizens. The teams will provide descriptions of current nonpoint source management activities within a basin, conduct assessments of nonpoint source controls in targeted watersheds, prioritize impaired waters for development and implementation of restoration strategies and determine issues for remedial action. The teams will develop 5 year action plans to reflect these priorities.

General management strategies in the Albemarle-Pamlico basin include proper maintenance and annual inspections of onsite waste disposal systems such as septic tanks; maintenance and repair of sanitary sewer lines; elimination of direct unpermitted discharges of domestic waste; proper management of livestock to keep wastes from reaching surface waters; encouragement of local health departments to routinely monitor waters known to be used for swimming; and implementation of marina BMPs and the installation of pumpout stations at all marinas.

In the Barataria-Terrebonne Estuaries, several initiatives are underway including the production of a video and brochure regarding proper sewage disposal and maintenance of septic systems and individual treatment systems. The Gulf of Mexico is using this region as a pilot project in its Shellfish Challenge program, aimed at increasing harvestable oyster beds by ten percent.

Morro Bay has developed a list of priority sources and protection efforts are beginning to be implemented. These include: removal of illegally moored boats adjacent to the oyster beds, development of regular inspection programs for sewage lift stations, establishment of a "no discharge zone" in the southern reaches of the bay, enforcement of live-aboard ordinances, installation of new and more accessible pump-out stations, distribution of boater education literature, replacement of on-site septic systems with centralized sewerage, retaining stormwater wherever possible, and fencing cattle from direct access to creeks. A Technical Advisory Committee has been formed by the Regional Water Quality Control Board and is developing a bacteria monitoring plan and reviewing proposed action plans.

In the Charlotte Harbor region, many counties monitor pathogen levels at specific locations. In some cases, there is concern that more locations at increasing intervals should be sampled. However, local funding is frequently low for these programs. As a new NEP, Charlotte Harbor has yet to identify specific management actions to address pathogen contamination; however, water quality degradation, including pathogens, is a priority problem for the program.

In Puget Sound, a variety of partnerships have been established to address the problems associated with pathogens. Programs and permits for municipal wastewater treatment, stormwater, and combined sewer overflows are established in state and federal laws and are implemented by local governments. Agricultural practices, in contrast, rely heavily on voluntary participation by landowners with support from conservation districts, universities, and various government agencies. The management of on-site sewage systems relies on a partnership primarily involving local health jurisdictions, septic contractors, and property owners. And sewage issues associated with boating and marinas are addressed through private and public partnerships aimed at improving the availability of sewage pumpout facilities and educating boat owners.

Prior to the NEP, the City of Portland (Oregon) adopted a $750 million 20 year project to remove CSOs from the Willamette River. The Willamette River is the major discharge into the Columbia River. Other cities are adopting removal programs.

To top of page

A variety of management approaches are being undertaken by the National Estuary Programs. The following are some examples.

The Peconic Estuary will focus on water quality preservation; and promoting and enhancing best management practices such as STOP ("Stop Throwing Out Pollutant") programs, road runoff, integrated pest management, and stormwater management at marinas, golf courses, and other commercial facilities. Public education and outreach are integral to these efforts (e.g., use, misuse, and disposal of household hazardous products).

The Delaware River Basin Commission (DRBC), working with the states, federal agencies, and interested parties, is developing Total Maximum Daily Loads (TMDLs) and Waste Load Allocations (WLAs) for many of the toxic substances. USEPA is working with DRBC and the states to evaluate sources of PCBs from high volume low concentration sources.

In Morro Bay, pollution from boat yards and other urban sources can best be controlled through implementation of Best Management Practices and educational outreach. Boat yard owners have recently applied for general stormwater permits, but follow through on the implementation of practices should be encouraged by the Regional Board.

Corpus Christi is considering the following actions for inclusion in its plan: review of water quality standards, numerical criteria, and designated uses for all areas; establishment of biological criteria as a component of water and sediment quality criteria; establishment of wastewater discharge permits on a watershed basis; and development of a regulatory permitting process for mariculture operations.

The Casco Bay plan recommends educating boaters about low impact practices, nontoxic boat products, and the need to protect sensitive habitats; establishing a reduction and management program for toxic pollutants in communities and small businesses; conducting pollution prevention audits for businesses and industries that affect Casco Bay; developing a comprehensive management strategy for dredged material; and developing sediment quality criteria and discharge limits that apply to Casco Bay.

The Long Island Sound plan emphasizes 1) continued source control through NPDES permitting programs, pollution prevention, and watershed planning for nonpoint source runoff; 2) remediation of contaminated harbors where feasible, and 3) continued assessment of contamination levels, effects, and risks to improve management. Currently, USEPA, the 2 states, the National Marine Fisheries Service, and Army Corps of Engineers are cooperating in developing information for a Dredged Sediment Management Plan.

The New York-New Jersey Harbor plan seeks to reduce municipal and industrial discharges of chemicals of concern; minimize the discharge of toxic chemicals from CSOs, storm water, and non-point sources; reduce air emissions of chemicals of concern; remediate identified solid and hazardous waste sites; track-down and clean-up other sources of chemicals of concern; improve chemical/oil spill response and prevention; focus pollution prevention activities on chemicals of concern; establish consistent methodologies to assess risks and improve communication of fish advisories; and review and develop criteria for copper and other priority chemicals.

In the San Francisco Estuary region, the Regional Monitoring Program (being financed by dischargers at over $2 million per year) includes 68 agencies and organizations who work in partnership to understand and address contaminant issues; this Program also provides a forum for dischargers and regulators. A new interagency public/private coordinating committee was created in 1995 to attack pesticide toxicity problems in urban runoff. The Bay oil industry is developing new methods for reducing selenium discharges in order to meet a 50 percent reduction requirement by 1998. A new national public-private Brake Pad Partnership has been created to voluntarily reduce copper pollution of South Bay waters.

The Tampa Bay Program is addressing localized hot spots of contamination in the Bay by reducing sources of toxics within watersheds that drain to these hot spots. Toxic action plans being developed for priority drainage basins are expected to emphasize pollution prevention and stormwater treatment as the principal control measures, but may also include point source and air emission controls where cost effective opportunities exist.

In the Albemarle-Pamlico Sounds, point source discharges are controlled through the state's NPDES permit process. Municipalities with significant industrial users limit toxic substances through their pretreatment programs. Source reduction and wastewater recycling at STPs also reduces the amount of toxic chemicals being discharged to a stream. Whole effluent toxicity testing is required at regular intervals for major dischargers. Nonpoint sources of pollution are controlled through BMPs.

The Sarasota Bay Program, under a cooperative agreement with the Southwest Florida Water Management District, is working on a project to identify sources of contaminants to the Bay. The Program is also working with the University of Florida and the County Cooperative Extension Service offices to promote the Florida Yards and Neighborhoods Program and to conduct a study to evaluate the pesticide and nutrient removal rate of properties landscaped in an environmentally sensitive manner.

In Narragansett Bay, toxics are being addressed mainly through the NPDES programs. Dischargers are required to monitor for toxics and toxicity, and those having significant industrial wastes have, in most cases, developed pretreatment limits to require those industries to remove toxics before releasing them into the sewers. Monitoring of the sewer lines as well as levying fines has produced compliance from the "bad actors" who wish to avoid treatment, while education and outreach programs for industrial users have ensured voluntary compliance in most cases. Through a Hazardous Waste Reduction Project, initiated by the Narragansett Bay Estuary Program, environmental audits were conducted at a wide range of industrial sites that provided owners with recommendations on new, less toxic, and cost effective processes. Due to the success of this project, it has been instituted as an official state continuing program. It has also been recognized nationally as a highly effective and successful program capable of reaching out to the smaller business users who often do not have the capital or knowledge to hire engineers for technical advice on pollution reduction/elimination strategies.

The Puget Sound Plan takes a four-pronged approach to managing sediment contamination: adoption of sediment standards, source control through wastewater discharge permits and stormwater management, ranking and cleanup of sediment hot spots, and management of dredging for navigation and shoreline development.

In Santa Monica Bay, current loadings of toxic chemicals are addressed mainly through the NPDES programs. These include the pretreatment programs implemented by publicly owned treatment works and municipal and industrial stormwater programs. Sediment toxic hot spots formed by historical dumping of DDT and PCBs are now under USEPA Superfund investigation and are subject to a lawsuit for damage compensation/recovery filed by the federal and state Natural Resource Trustees. In addition, a regional coordinated monitoring program is being implemented to assess the status and trends in loadings of 12 toxic pollutants of concern from various point and nonpoint sources.

To top of page

A variety of management approaches are being undertaken by the National Estuary Programs. The following are some examples.

In the Delaware Estuary region, fragmentation and degradation of upland habitat is a land use issue that is traditionally handled at the local government level. The Delaware Estuary Program has proposed actions in its CCMP to assist local governments manage land better from an ecological perspective. A wetlands coordinator has been hired through the program who will take an estuary-wide approach to wetland restoration and management.

The Center for the (Delaware) Inland Bays is a unique experiment in government. Historically, the inland bays of Delaware were the subject of much conflict among environmentalists, developers, governmental agencies, marina operators, farmers, and others. The original program was placed within an agency with regulatory authority and was often in conflict with groups not wishing to be regulated. The result was a clear lack of trust among constituency groups. A consortium of concerned citizens committed to saving the bays formed and developed a new structure. Recognizing the importance of the collaborative process that led to the CCMP, Delaware's General Assembly and Governor Carper enacted the Inland Bays Watershed Enhancement Act in 1994. The Act established the Center for the Inland Bays to oversee and facilitate both the implementation of the CCMP and long-term approaches to the wise use and enhancement of the watershed. USEPA serves on the Board of Directors as an ex-officio member and the Act also encourages the membership of other federal agencies. The Center has begun to oversee CCMP implementation and address additional environmental needs in the watershed.

In Long Island Sound, USEPA, the States of New York and Connecticut, New York City, U.S. Fish and Wildlife Service (USFWS), National Marine Fisheries Service, New York Sea Grant, and Save the Sound, Inc. (a Sound-wide nonprofit organization) are working together to develop a Bi-state Habitat Restoration Strategy.

The Commonwealth of Massachusetts has established a complex structure of laws and regulations to combat wetlands loss in the Massachusetts Bays region. The cornerstone of the state's current Wetlands Protection Program is the Wetlands Protection Act which established a public review and decision-making process to preserve the state's dwindling wetlands. Although this is considered to be one of the Nation's most effective wetlands protection programs, the State has not been able to completely stem wetlands loss due in part to legal exemptions, unsuccessful mitigation practices, and limitations of municipal government.

The Rhode Island Coastal Resources Management Council (RI CRMC) has developed a regulatory framework which tries to balance development pressures with some control over impacts to the coastal zone and provides public meetings and workshops concerning its work. The Narragansett Bay Estuary Program (NBEP) works with RI CRMC to help educate the public on the need for such controls. Efforts are expected to increase concerning nutrient-related impacts in the next several years. The University of Rhode Island (URI) Coastal Resources Center (CRC), Graduate School of Oceanography, and Department of Natural Resources Sciences (DNRS), as well as RI Sea Grant, are significant partners with both the RI CRMS and NBEP to provide outreach materials, as well as technical help. Recent partnerships by NBEP, Save The Bay, URI, USFWS, and NOAA have led to the initiation of several pilot projects to attempt habitat restoration through eelgrass transplants in certain areas of the Bay. In addition, NBEP, Save The Bay, and USFWS have been actively pursuing funds to allow for the identification and mapping of coastal natural resource areas on a high resolution scale, as well as the initial planning for future habitat restoration efforts.

In Barnegat Bay coastal wetlands were mapped and protected under the New Jersey Coastal Wetlands Act of 1970. NJDEP is currently developing more precise information on inland wetland locations through an ongoing program of mapping with field verification. There has been a concerted effort to acquire marsh islands still in private ownership using a consortium of government and nonprofit agencies, especially the Trust for Public Land. Using some of the money set aside for acquisition from the Ciba-Geigy donation, now in a dedicated fund, New Jersey recently purchased Sedge Island, the site of a fishing/hunting club near Barnegat Inlet. This cooperative method will be continued. As a beginning to devising management tools for corridors, the NJDEP's Endangered and Nongame Species program with funding from New Jersey's Coastal Management Program is developing a "Landscape Model" program in Cumberland and Cape May Counties which will be transferable to this watershed. With the existence of the Ciba-Geigy acquisition fund, the New Jersey Green Acres funds, and nonprofits experienced in acquisition methods in the area, wildlife corridors will be a primary focus of the Management Conference.

Basinwide ecosystem plans are being developed for the Albemarle-Pamlico Sounds. Accurate maps and records of wetlands, fisheries habitats, federal and state endangered species/habitats, natural areas, and natural communities are developed and maintained for the region. Areas identified as having the highest priority for protection are brought into public ownership. The ability of state and federal agencies to enforce existing wetlands regulations is being enhanced. Regulatory programs to protect vital fisheries habitats are being strengthened. An expanded program to restore wetlands is being developed and implemented and a mitigation program to compensate for unavoidable permitted wetland losses is being established.

The Indian River Lagoon (IRL) CCMP includes several actions to protect, preserve, and enhance remaining habitats as well as to restore damaged habitats. In recent years, efforts have been initiated to protect and preserve the remaining natural communities. Acquisition programs have been established at the federal, state, and local level to purchase and protect lands that have been deemed ecologically valuable. These efforts have fostered many cooperative efforts to acquire key parcels of land. Restoration of marshes impounded for mosquito control has resulted in a partnership between the St. Johns River Water Management District (SJRWMD), the South Florida Water Management District (SFWMD), and the various mosquito control districts. The water management districts have provided funding to the mosquito control districts through the SWIM program for the purchase and installation of culverts and other equipment to implement improved marsh management strategies, resulting in the reconnection of these marshes to the IRL.

There are many organizations and agencies working together to address the serious problem of wetland loss in the Barataria-Terrebonne region. The Barataria-Terrebonne National Estuary Program (BTNEP) has developed and is implementing a CCMP containing several action plans that address the problems leading to habitat loss. Many agencies and organizations are contributing to CCMP implementation. The Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) is funding numerous wetland management/enhancement projects aimed at reducing the rate of vegetated habitat loss. The Louisiana Department of Natural Resources (DNR) Coastal Zone Management Division evaluates activities being conducted in the wetlands to determine if the activity will have detrimental impacts. Mitigation of some type is often required of the permit applicant. The Coalition to Restore Coastal Louisiana, USEPA, Department of Environmental Quality (DEQ), Cooperative Extension Service, and many other organizations and agencies are playing major roles in educating the public on wetland loss issues. Act 6 was passed in 1989 by the Louisiana voters to establish the Coastal Restoration Trust Fund and the Louisiana Coastal Wetlands Task Force to address wetlands loss.

In the Corpus Christi Bay area, habitat protection in general suffers from the lack of a regional (or ecosystem scale) perspective of habitat areal extent and function. Local governments tend not to consider habitat protection in land use planning/zoning. Federal agencies, on the other hand, are mostly focused on the management of federal lands. More effort is needed in creating partnerships between local, state, and federal agencies - with assistance and resources from the private and nonprofit sectors - to make habitat management a more holistic effort with goals and objectives which extend beyond immediate, local jurisdiction and interest.

The CCMP for Galveston Bay identifies issues related to wetland habitat protection as the highest priorities. The CCMP outlines a coordinated ecosystem approach including the following actions:

• Restore, create, and protect wetlands (HP-1).
• Promote beneficial uses of dredged material to restore and create wetlands (HP-2).
• Inventory degraded wetlands and fund remedial measures (HP-3).
• Implement a coordinated system-wide wetland regulatory strategy (HP-4).
• Acquire and protect quality wetlands (HP-5).

The Sarasota Bay CCMP recommends restoration and enhancement of wetlands, rather than just protection, as a guiding policy. To facilitate this shift in emphasis, the SBNEP has developed a comprehensive approach to wetlands restoration and has prioritized sites for restoration. Sites will be restored on an ongoing basis and as funding becomes available. The Florida Department of Environmental Protection (FDEP) and the Southwest Florida Water Management Division are working with the SBNEP and local governments in designing and constructing habitat restoration projects. The U.S. Army Corps of Engineers has committed significant resources to restoring areas throughout the Bay which were created from Corps of Engineers dredge and fill activities. USFWS has provided significant funding for restoring and enhancing intertidal wetlands. The Surface Water Improvement and Management Program has committed technical assistance for habitat restoration projects.

The Tampa Bay CCMP establishes goals of restoring 12,350 acres of additional seagrasses baywide and 1,800 acres of low-salinity wetlands at a minimum rate of 100 acres every five years to "restore the balance" of wetland types. The seagrass restoration target will be achieved by capping nitrogen discharges to the bay at existing levels. The Nitrogen Management Consortium, described under NUTRIENTS, is the public/private partnership through which an equitable and cost-effective nitrogen management strategy will be developed. The SWFWMD Surface Water Improvement and Management (SWIM) department will take the lead in wetland restoration and protection (through land acquisition) with support from the Florida Department of Environmental Protection, Florida Game and Fresh Water Fish Commission, and local governments.

Current planning practices in the Lower Columbia River area are inadequate to address the impacts of future growth because they do not deal with cumulative impacts, do not assure that adequate infrastructure is in place before development occurs, do not deal with conflicting uses except to try to keep them separated, and do not manage human development in terms of its relationship with the larger ecosystem. Future growth will be managed in a way that enhances the quality of life for the biological and human communities. Management goals include: maintenance of economic vitality and biological integrity; encouragement of economic activity that is helpful to the ecosystem; and proactive land use planning instead of reactive, so that cumulative impacts can be anticipated and planned for, taking into consideration the carrying capacity of the land and technological solutions to problems caused by population growth.

There are several ongoing efforts to better protect wetlands in the San Francisco Estuary. The San Francisco Estuary Regional Water Quality Control Board is beginning to prepare a regional wetlands management plan, as called for in the CCMP. As a first step, a dozen state and federal agencies, with assistance from more than a hundred biologists and other scientists, are developing regional wetlands habitat goals to form the basis of the plan. The Save San Francisco Estuary Association has initiated the Partnership for the San Pablo Baylands to develop non-regulatory approaches to wetlands protection with local landowners in the North Bay. The San Francisco Estuary Joint Venture has formed as a public-private partnership among 28 government and special-interest groups to help acquire, restore, and protect wetlands on a regional scale. USEPA has initiated its North Bay Initiative and Forum to work with stakeholders in the North Bay towards developing better wetlands protection. The Bay Conservation and Development Commission, with USEPA funding, is working with city and county governments in the North Bay to strengthen local wetlands protection planning efforts. Through the CALFED process, public and private interests are identifying measures to address water quality and reliability issues in the Sacramento-San Joaquin Delta. A part of the solution to these problems will include the restoration of wetlands in the Sacramento-San Joaquin Delta and in San Francisco Bay. The S.F. Bay Regional Water Quality Control Board, in cooperation with the U.S. Army Corps of Engineers and the S.F. Bay Conservation and Development Commission, has undertaken a Bay Area Regulatory Pilot Project to streamline the permitting process for projects impacting wetlands, while strengthening wetlands management and protection. The program's primary objectives are: assessing the feasibility of State assumption of Section 404 permitting from the Federal government; evaluating the potential consolidation of Section 404, 401, and BCDC permits; and developing an improved permitting process that will provide better service to applicants.

A 1995 update to the S.F. Bay Regional Water Quality Control Board's San Francisco Bay Water Quality Control Plan included several improvements to wetlands protection, many of which were recommended in the CCMP. Among the recent additions to the Basin Plan are a "no net loss" policy, a wetlands alteration policy addressing wetlands fill and hydrologic modification, clarification of wetlands as "waters of the State," a mitigation policy, and a policy on the use of dredged material to restore wetlands.

The Long-Term Management Strategy for Dredging continues to explore ways to maximize the beneficial reuse of dredged material, which may include significant new efforts to use dredged material for wetland enhancement and restoration.

The S.F. Estuary Project's Delta In-Channel Islands Workgroup has drafted a "Coordination of Efforts" document stipulating a commitment to protecting approximately 800 islands, which are home to fish, wildlife, wetland and riparian plants, and numerous special status species. The non-binding document is now being circulated among interest groups, agencies, and landowners.

In the Charlotte Harbor Study Area, there is renewed interested in the problem of habitat loss including attention to land acquisition opportunities and development of an Integrated Habitat Network in the Upper Peace River basin. Additional management approaches include: Endangered Species Act, net ban and fisheries management quotas, game management practices, growth management, and development of a regional impact review process.

The Morro Bay National Estuary Program (MBNEP) is working on a watershed-based approach to sediment pollution, with most effort focused on changes in land management practices and reestablishment of flood plains. Studies of bay hydrodynamics may suggest in-bay approaches to the sedimentation problem. The program is exploring the establishment of conservation/mitigation banking as a method of reducing fragmentation and maintaining significant parcels of coastal dune scrub habitat. Protection of riparian and creek corridors is of high priority, particularly through grazing management programs, development of conservation easements for buffer areas, and revegetation programs. Wetland restoration can be integrated with stormwater and wastewater treatment facilities to increase habitat while improving water quality.

The Puget Sound Work Management Plan seeks a balanced approach using land use planning, regulation, mitigation, enhancement, and acquisition. Coordination among and between state and federal agencies has improved, but needs to go further. There have been some excellent examples of cooperative efforts to restore habitats. Spencer Island, the largest wetland restoration project in the Pacific Northwest, was a collaborative effort with funding and technical assistance provided by local, state, and federal agencies, as well as private groups.

Education is a vital piece of habitat protection. There are efforts underway in the Puget Sound area to share knowledge about successful bioengineering projects on rivers and marine shorelines. Local groups, such as "Water Watchers" and "Stream Teams," work to educate local citizens about water and habitat issues and provide volunteer opportunities for participants to put their new knowledge to work.

To top of page

A variety of management approaches are being undertaken by the National Estuary Programs. The following are some examples.

In Sarasota Bay, civic and environmental organizations have adopted wetland sites and are controlling the encroachment of invasive species in these areas. Local governments are beginning to promote the planting of native vegetation while promoting the removal of exotic vegetation through the comprehensive planning process.

The U.S. Army Corps of Engineers has been the leader in research and control of introduced aquatic plants. Continuation of its program, especially biological control research, is critical to the long term management of introduced plants in the Barataria-Terrebonne estuaries. USDA has a nationwide Noxious Weed List; species on the list cannot be imported to the U.S., with the exception of some limited research purposes. The Louisiana Department of Fish and Wildlife (LDFW) has developed brochures to educate citizens about the impacts of introduced plants and to encourage the use of native species when possible. The Louisiana Sea Grant College Program and the U.S. Fish and Wildlife Service are joint sponsors of the Southern Region Zebra Mussel Newsletter; a task force monitors the influx of zebra mussels into the lower Mississippi River. The LDWF and Louisiana Fur and Alligator Advisory Council have been encouraging the development of a private fur corporation, to provide a continuous supply of nutria pelts in large numbers year-round.

The Barataria-Terrebonne Estuaries is pursuing the following additional ideas: 1) to control introduced plant species: ban the sale of Chinese tallow trees; develop a noxious weed law for the state; develop biocontrol methods; designate areas of exotic infestation to demonstrate removal and replanting projects; and encourage nurseries to grow native species for private landscaping; 2) to manage zebra mussels: establish a task force to provide leadership on the issue; initiate a monitoring program; assess potential locations for zebra mussel settlement; examine various control measures; and begin a research and development program on controls and beneficial uses; and 3) to control nutria: support the private fur corporation; solicit support from legislators; continue aerial surveys; and encourage development of a tanning industry.

Corpus Christi is considering the following actions for inclusion in its plan: development of a regulatory permitting process for mariculture operations (only two shrimp farms in Texas have wastewater discharge permits); education of ship owners/operators regarding the National Invasive Species Act; and determining the risks posed by invasive species contained in vessels that are servicing Port Corpus Christi.

The Tampa Bay NEP provided seed money to a local homeowners association to develop a Brazilian pepper brochure, entitled "Beautiful but Bad", for distribution to other citizens with shoreline homes. It has been one of the most popular public outreach tools and provides homeowners with information about how to identify and eradicate this species and where to get help. Additionally, the Tampa Bay NEP's habitat restoration master plan includes efforts to eradicate and manage exotic species on public lands, a key issue along Florida's coastline.

An assessment of the existing status of marine aquatic invasives is necessary and funding for this study will be sought during the National Estuary Program planning process. A major oil receiving terminal north of Morro Bay represents a significant risk for invasive species introduction. This issue is being addressed during the environmental review process for the terminal lease from the California State Lands Commission. Also, a proposed terrestrial pipeline may eliminate the need for this terminal entirely. Native fresh water resources can be enhanced and favored over introduced species by restoration of aquatic habitat. Other possible approaches under consideration include development of recreational fisheries for introduced fish species. Improved grazing management practices and roadside maintenance procedures can be effective at reducing nuisance thistle populations. Management of hoary cress and german ivy will be difficult and requires the development of effective methodologies, but should be established as a management priority for managing agencies.

To top of page

A variety of management approaches are being undertaken by the National Estuary Programs. The following are some examples.

In the Albemarle-Pamlico Sounds region, water control structures placed in drainage ditches allow the land users to exert some control over the level of the water table in fields. This process can result in more efficient drainage and may improve water quality draining to receiving waters. The North Carolina Division of Soil and Water Conservation administers the Agriculture Cost Share Program which provides incentives to farmers to install best management practices (BMPs) by offering to pay up to 75 percent of the average cost of approved BMPs. Since inception of the Program in 1985, more than 2,600 water control structures have been installed within the five river basins of the watershed. These water control structures are serving about 200,000 acres of agricultural land in this region.

In the Charlotte Harbor study area, a watershed approach to surface water management will result in a watershed management plan for each drainage basin, including establishing minimum flows and water levels for each water body. Water Management Districts are responsible for establishing minimum in-stream flows so that permitted water withdrawals do not adversely impact natural resources. The Florida Department of Environmental Protection and the Water Management Districts regulate groundwater withdrawal for water supply, agricultural, and industrial purposes. Point source discharges, such as sewage treatment plants and industrial facilities, are regulated for water quality, and flow quantities are also monitored. BMPs are encouraged to decrease and retain stormwater runoff and water use permits are administered to control water use. The Florida Yards and Neighborhoods Program and Xeriscaping are education programs for residential communities to improve the quality of runoff and decrease water use for landscaping.

The primary purpose of the Caloosahatchee Watershed Program (Charlotte Harbor), run by the Water Management District, is to protect and enhance this critical ecosystem through the development of a plan that addresses restoration and water supply while maintaining and enhancing the estuary within the context of continued urban, agricultural, and recreational use of water resources.

The St. Johns River Water Management District (SJRWMD) and the South Florida Water Management District (SFWMD) have a legislatively mandated partnership for the management of the Indian River Lagoon (IRL) and have taken leading roles in the development and implementation of the IRL CCMP. Both have developed partnerships with local governments in their respective areas, offering grants for the establishment of stormwater utilities, promoting the use of BMPs, and funding projects to upgrade older drainage systems. In the southern portion of IRL, U.S. Army Corps of Engineers (USACE), working with SFWMD, is undertaking a study to determine the feasibility of modifying federal drainage projects to reduce their impact on the IRL. This effort is part of the re-study of the federal Central and South Florida Project. In the northern portion of the IRL, SJRWMD has assumed the costs of pollutant load reduction goal (PLRG) development. In the southern portion, PLRG costs will be shared by the SFWMD and USACE. The costs of implementation of the PLRGs will largely be borne by local governments with assistance from USACE, USEPA, the Water Management Districts, and other agencies.

The management of freshwater resources in the Corpus Christi Bay system needs to be carried out within the framework of a regional, holistic approach that includes environmental needs. A holistic management approach will attempt to deal with (at a minimum): infrastructure for wastewater reuse, other return flows to the estuary, freshwater inflow, watershed management, affordable water supply, in-stream needs, wetland and other habitat preservation, demand management, urban runoff management, atmospheric loading, industrial treatment, municipal treatment, total estuarine productivity, conjunctive use, sustainable development, water permitting/reallocation, onsite sewage facilities, water recreation, conservation, data acquisition, meteorological studies, public education, and bay circulation.

In the Corpus Christi Bay region, management of freshwater inflow is currently a local and state government issue, and requires an agreed upon process for decision-making. The current decision-making framework is politically and emotionally charged, and more "crisis management" than proactive in nature.

Although the volume, timing, and quality of freshwater inflows to the Galveston Bay estuary are important factors in its health, there is no statutory mechanism in Texas to provide for the necessary freshwater or circulation. Inflow to Galveston Bay is dealt with on a case by case basis advocacy process with the state environmental agency. Increased demands of a growing population, historic grants of water rights, and periodic droughts make management a difficult challenge.

A major component of the Sarasota Bay CCMP recommends the construction of a multi-jurisdictional regional wastewater reuse system. The overall plan is to reclaim approximately 50 mgd of wastewater for agricultural, urban, and possibly potable use. The wastewater will be predominately returned to the Manatee River watershed (in the Tampa Bay region) which has historically received attention due to the lack of freshwater inflow. A multi-jurisdictional task force has been established, chaired by the Southwest Florida Water Management District (SWFWMD) to complete the final design of the wastewater recovery system. Funding is being provided through Congressional appropriation, SWFWMD, and local governments.

A major goal of the Tampa Bay CCMP is to restore up to 1,800 acres of low salinity habitats, a portion of which can be achieved by re-establishing adequate freshwater inflow from four impounded tributaries. SWFWMD has requested the Tampa Bay NEP to help facilitate that process by convening a Minimum Flow Advisory Group to develop technically sound recommendations for determining ecological criteria necessary to set minimum flows on the two highest priority rivers.

The Morro Bay NEP has primarily been seeking solutions to fresh water inflow problems within the system of appropriative water rights. A flow study will be conducted as part of the program which will provide a framework for making management decisions regarding fresh water flows. As new water sources become available, they should be utilized, at least in part, to offset existing overdiversion, rather than be applied directly to increased municipal development. A new source of water is anticipated in the near future from the State Water Project, which will provide some opportunities for restoring instream flows. Both the City of Morro Bay and the community of Los Osos have opportunities for reclamation of wastewater to supplement instream flows. Though water quality will certainly be of concern, the water quantity provided by these discharges is generally regarded as an asset in this water short area. Another issue of concern for creek resources has been the fluctuating levels of flow resulting from wastewater plant discharges. The National Estuary Program has worked with the California Men's Colony and the County of San Luis Obispo to reduce this fluctuation as mitigation for increased diversion.

In the San Francisco region, recent management changes are promoting more efficient use of limited water supplies and encouraging water recycling. New amendments to the California water code prohibit the use of drinking water for watering parks, cemeteries, golf courses, and highways. Tougher criteria for water efficiency and management plans are required for the 100 districts using Central Valley Project water. There is recent consensus for more efficient agricultural water management practices to be adopted by numerous agricultural water districts via a Memorandum of Understanding. There is more proactive interest in land use management issues by water districts concerned about the quality and quantity of their water supplies (watershed management planning to reduce impacts from new development, urban runoff, grazing, and other factors). Over 650,000 acre feet of Bay area wastewater could be recycled on a regional basis by the year 2020 under four options proposed by the Central Valley Recycling Project.

To top of page

A variety of management approaches are being undertaken by the National Estuary Programs. The following are some examples.

Regional fishing pressures and regulations are outside the scope of the Peconic Estuary Program (PEP) management objectives. However, PEP has committed to improving habitat within the estuary. The PEP Living Resources Committee is an active coalition, comprised of the state Department of Environmental Conservation, USFWS, Nature Conservancy, Cornell Cooperative Extension, and other agencies. Ultimately, partnerships with local governments in land use management actions will also be critical.

To protect fishery resources in the Albemarle-Pamlico Sounds, management plans will be developed and implemented for fisheries that are important to recreational and commercial fishing interests, including recovery objectives for depleted stocks. The existing marine fisheries license structure will be modified to improve data collection with respect to landings, demographics and fishing effort, and to generate increased revenues for fisheries management. The development of bycatch reduction gear and practices will be continued and their use will be required. A cost share program for best fishing practices for commercial fishing gear will be instituted.

In recent years, efforts have been initiated to protect and preserve the remaining communities within the Indian River Lagoon basin. Acquisition programs have been established at the federal, state, and local level to purchase and protect lands that have been deemed ecologically valuable. These efforts have fostered many cooperative efforts to acquire key parcels of land. Restoration of marshes impounded for mosquito control has resulted in a partnership between the St. Johns River Water Management District (SJRWMD), South Florida Water Management District (SFWMD), and the various county mosquito control districts. The WMDs have provided funding through the SWIM program for the purchase and installation of culverts and other equipment to implement improved marsh management practices, restoring the connection of these marshes to the IRL.

Each of the three states in the Delaware Estuary region has its own fish and wildlife management units within state government. In addition, the Delaware River Basin Fish and Wildlife Management Cooperative currently works with the basin states on issues related to anadromous fish and the Mid-Atlantic Fisheries Management Council and the Atlantic States Marine Fisheries Commission address multi-state fisheries issues. The U.S. Fish and Wildlife Service has responsibility for certain threatened and endangered species. Shorebirds and horseshoe crabs seem to be two species that the interested agencies are likely to address on an estuary-wide basis.

Much is being done by state and federal agencies and other entities to address the problems facing the living resources of the Barataria-Terrebonne region and to lessen the threats to these resources. The BTNEP has developed a CCMP which contains many action plans that address the problems associated with the depletion of living resources. The Department of Environmental Quality (DEQ) is monitoring nutrient, bacteria, and toxic contaminant loads in waterbodies in an attempt to lessen the threats that these pollutants pose. The U.S. Coast Guard, USEPA, and DEQ have rules and regulations intended to prevent spills of petroleum and other oil field products and are responsible for responding to spills that do occur. Louisiana state agencies are trying to prevent sewage pollution and agricultural pollution through monitoring, rules, and regulations. Many agencies are pushing for and implementing plans for the preservation and restoration of habitat and breeding grounds for living resources. The Department of Wildlife and Fisheries regulates harvesting of species and monitors populations to prevent depletion of the resources through overharvesting. The Gulf of Mexico Program's Shellfish Challenge Project is aimed at increasing the harvestable oyster grounds in Louisiana by 10 percent; a pilot project is being conducted in the study area.

In the Corpus Christi Bay region, management priority should be placed on gaining knowledge where it is lacking and in those areas of greatest known impacts, such as habitat loss or dredging. The U.S. Army Corps of Engineers (USACE) is working closely with the NEP to develop alternative maintenance dredging schedules and techniques and new methods to create beneficial uses of dredged material. The Natural Resource Conservation Service (NRCS), National Marine Fisheries Service (NMFS), U.S. Fish and Wildlife Service (USFWS), SeaGrant, and others are assisting in these efforts. State agencies with responsibility for fish and wildlife management are heavily invested in the CCBNEP planning effort.

The Sarasota Bay NEP concluded that the loss of habitat was directly related to the decline of fisheries in the Bay. Therefore, the CCMP calls for the restoration of these habitats. For seagrass habitat, nitrogen pollution from wastewater and stormwater runoff has been targeted, while restoration has been promoted to restore saltwater wetlands. SBNEP is working with local governments to improve overall water quality in the Bay.

While there is no substitute for natural habitat with respect to the diversity and productivity of organisms, for some environments (e.g., dredge holes, canal communities, channel markers), engineering options exist that can create artificial habitats for juvenile and adult finfish, shellfish, and invertebrates. The Sarasota Bay Comprehensive Artificial Habitat Enhancement Plan describes a long-term program for testing, implementing, and monitoring such fishery enhancement modules throughout the region.

Efforts by the Tampa Bay NEP to protect and enhance Tampa Bay's diverse fish and wildlife resources focus primarily on establishing healthy environments through improvements in water quality and habitats. A key effort of the NEP and its partners in 1997 will be to develop recommendations for manatee protection in Tampa Bay and to seek ways to increase allocations for marine law enforcement from existing saltwater fishing license revenues.

One goal of the Lower Columbia River NEP is the biological sustainability of populations of native fish and wildlife, concurrent with population and economic growth. This will be measured by the following: removal of threatened and endangered listings; continued contributions of the river to the economy of the area; and creation of a state of equilibrium in the river that protects both biological diversity and economic productivity.

Many of the declines observed in fish and wildlife populations are a direct or indirect result of habitat loss and degradation in Morro Bay. Habitat protection and restoration activities in Morro Bay include development of buffer areas around riparian corridors; reestablishment of fresh water flows; reduction of sedimentation of instream, brackish and salt water habitat; and development of mitigation and conservation banking programs for wetlands, riparian habitat, and coastal dune scrub. Declines which are suspected as a result of overexploitation need better documentation before action can be taken. Additional funding may be required to assess the status of specific species. The National Estuary Program is funding a bay habitat study to qualitatively describe the flora and fauna associated with various habitat types and provide further direction for additional studies.

In the San Francisco Estuary, a federal-state "operations group" of export pump managers and scientists was established in 1995 to make day-to-day decisions about pumping to minimize the loss of endangered species and negative environmental impacts. There has been a major expansion of "real-time" (in the water) monitoring of fish movements and conditions in the Estuary to aid with daily water management. The cooperative federal-state CALFED Bay-Delta Program was created in 1995 to develop a long-term solution for balancing all beneficial uses of Estuary waters by fish and humans. The Bay-Delta Accord and the resulting State water quality plan have led to a shift from flow to salinity-based standards to protect the Delta environment. Adequate flows must be released to keep the 2 ppt isohaline (parts per thousand of salt in the water) within a certain range of positions in the Estuary near the Carquinez Strait that are associated with abundance in fish and biota.

There has also been a shift from single to multi-species recovery planning for endangered species protection. For example, a Delta Native Fishes Recovery Plan was completed in summer 1996 for seven species, including the endangered Delta smelt, the Sacramento splittail, and two runs of chinook salmon. There has been follow-up on the 1992 Central Valley Project Improvement Act mandates to double anadromous fish populations, including the recent completion of an Anadromous Fish Restoration Plan; improved flows for fish on the Sacramento, American, and Stanislaus rivers; planning for use of 800,000 acre-feet per year dedicated to fish under the act; and funding screens at water diversions associated with fish mortality.

Approaches taken by the Santa Monica Bay NEP to protect and enhance the Bay's habitat and living resources include restoring and increasing the quantity and quality of fish and wildlife habitats, ensuring the survival and recovery of endangered species, and educating and involving the public. The NEP seeks to identify cost effective methods to rebuild declining populations of "key species", augment existing and create new habitat reserves, increase the number of wildlife protection officers, and encourage citizen monitoring and reporting.

To top of page

General Information & Resources En Español

EPA Home | Privacy and Security Notice | Contact Us