National Estuary Program: A Collaborative Approach to Protecting Coastal Water Quality

National Estuary Program: A Collaborative Approach to Protecting Coastal Water Quality

97-644 ENR
CRS Report for Congress
Received through the CRS Web
National Estuary Program:
A Collaborative Approach to
Protecting Coastal Water Quality
Updated January 12, 2001
(name redacted)
Environmental Information Analyst
Resources, Science, and Industry Division
Congressional Research Service ˜ The Library of Congress

National Estuary Program: A Collaborative
Approach to Protecting Coastal Water Quality
Summary
Estuaries are coastal bays or rivers and their freshwater tributaries. These
waterways provide resources for diverse uses including commerce, public
infrastructure, and recreation. The Clean Water Act Amendments of 1987 (P.L. 100-
4) established the National Estuary Program to identify nationally significant estuaries
that are threatened by pollution, land development, or overuse, and to award grants
that support the development of comprehensive management plans to restore and
protect them. State governors can nominate estuaries within their states to be
admitted into the National Estuary Program, and a total of 28 estuaries have been
admitted thus far. The Environmental Protection Agency (EPA) collaborates with
other federal agencies, state and local governments, non-profit institutions, industry,
and citizens to address an estuary’s environmental problems.
Appropriations for the National Estuary Program have ranged from an initial
funding level of $11.1 million in FY1987 to a high of $17.9 million in FY1992. The
current funding level for FY2001 is $13.8 million, the same amount as enacted for
FY2000. The Clean Water Act Amendments of 1987 originally authorized funding
for the National Estuary Program through FY1991, but Congress continued to fund
it through FY2000 without enacting reauthorizing legislation. The 106th Congress
enacted the Estuaries and Clean Waters Act of 2000 (P.L. 106-457), which
reauthorized the program at $35 million annually from FY2001 to FY2005. The law
also amended the Clean Water Act to allow funding to be used for implementing as
well as developing estuary management plans.
Apart from the National Estuary Program, P.L. 106-457 also authorized a total
of $275 million in matching funds from FY2001 to FY2005 for a new estuary habitat
restoration program to be carried out by the Army Corps of Engineers. The goal of
the program is to restore 1 million acres of estuary habitat by 2010. It would be a
new potential source of funding for implementing approved management plans under
the National Estuary Program. However, the total funding level of $275 million is an
authorized amount, which still must be appropriated by Congress before it would
become available.
While geographic and demographic factors differ among estuaries in the National
Estuary Program, many of them share the following environmental problems:
eutrophication, contamination from toxic substances and pathogens, habitat loss,
altered freshwater inflows, and endangered and non-native species. Common sources
of these problems include industrial pollution, wastewater overflows, stormwater and
agricultural runoff, waste from boaters and swimmers, land development, and
freshwater diversion. EPA has approved the management plans for 22 estuaries in the
National Estuary Program, and many interests are working together to address the
above environmental problems. While the program’s collaborative nature offers
flexibility, achieving results can require significantly more time than instituting
conventional regulatory measures. Its long-term success will depend on the continued
participation, commitment, and resources of the stakeholders in each locality.

Contents
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Why Should We Protect Estuaries? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
How Does the National Estuary Program Function? . . . . . . . . . . . . . . . . . . . . . 3
Appropriations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
What Are the Common Environmental Problems? . . . . . . . . . . . . . . . . . . . . . . . 6
Eutrophication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Toxic Substances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Habitat Loss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Altered Freshwater Inflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Endangered Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Non-Native Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
What Has the National Estuary Program Accomplished? . . . . . . . . . . . . . . . . . . 9
Puget Sound . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Reducing Pollution from Stormwater Runoff . . . . . . . . . . . . . . . . . . . 9
Restoring Habitats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Monitoring Water Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Involving and Educating the Public . . . . . . . . . . . . . . . . . . . . . . . . . . 10
San Francisco Bay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Restoring Wetlands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Managing Water Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Disposing of Sediments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Monitoring Water Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Albemarle-Pamlico Sound . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Setting Daily Limits on Discharges of Pollutants . . . . . . . . . . . . . . . . 11
Controlling Agricultural Runoff . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Managing Wastewater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Restoring Habitats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Long Island Sound . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Lowering Inputs of Nitrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Reducing Pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Managing Toxic Substances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Cleaning Up Floating Debris . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Selected References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

List of Figures
Figure 1. National Estuary Program Grant Funding: FY1987 to FY2001 . . . . . 6
List of Tables
Table 1. Status of the National Estuary Program as of January 2001 . . . . . . . . . 4

National Estuary Program: A Collaborative
Approach to Protecting Coastal Water Quality
Introduction
The Clean Water Act Amendments of 1987 (P.L. 100-4) established the National
Estuary Program to identify nationally significant estuaries that are threatened by
pollution, land development, or overuse, and to award grants that support the
development of comprehensive management plans to restore and protect them.1 The
Estuaries and Clean Waters Act of 2000 (P.L. 106-457) reauthorized the program
through FY2005 and amended the Clean Water Act to allow funding to be used for
implementing such plans in addition to developing them. The Environmental
Protection Agency (EPA) works with federal agencies, state and local governments,
non-profit institutions, industry, and citizens to address an estuary’s environmental
problems. Experience from past federal efforts were instrumental in the creation of
the National Estuary Program. The Chesapeake Bay and Great Lakes programs have
been studying water quality since the 1970s, and EPA and the National Oceanic and
Atmospheric Administration (NOAA) jointly studied water quality in six estuaries
from 1985 to 1987 that are now part of the National Estuary Program.2
The land draining into an estuary is its watershed, and the activities that occur
within it can affect water quality. The National Estuary Program is a watershed
approach in which all affected interests participate in creating solutions that balance
environmental objectives with competing issues. A watershed approach strives to
manage the water resources of a specific geographic area as opposed to federally
regulating certain sources of pollution uniformly. While this approach offers the
flexibility to design solutions within the context of local needs, stakeholders must
participate in the process and commit their time and resources for it to succeed.
This report is based on 11 of the 28 estuaries that are currently in the National
Estuary Program which represent common environmental problems along the nation’s
coastline: on the Pacific Coast, the Columbia River, Puget Sound, San Francisco Bay,
and Santa Monica Bay; on the Atlantic Coast, Albemarle-Pamlico Sound, Long Island
1 Estuaries are coastal bays or rivers and their freshwater tributaries. Because the
concentration of environmental problems is different in each locality, the extent of the
waterways and size of the land area that define each estuary in the National Estuary Program
vary. Consequently, the boundaries of some estuaries in the program are broader and further
inland than others.
2 EPA administers separate programs under sections 117 and 118 of the Clean Water Act to
address environmental problems in Chesapeake Bay and the Great Lakes.

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Sound, Narragansett Bay, and Maryland’s coastal bays (excluding Chesapeake Bay);
and on the Gulf of Mexico, Charlotte Harbor, Corpus Christi Bay, and Sarasota Bay.3
Why Should We Protect Estuaries?
Estuaries provide resources for diverse uses that many sectors of the public
value. However, overuse and improper management can degrade water quality and
limit an estuary’s productive capacity. In Section 320 of the Clean Water Act,
Congress stated that long-term planning and management are necessary to sustain the
productivity of estuaries and maximize their utility to the nation.
Estuaries support many commercial activities. The shipping industry is a large
source of employment and is an integral part of the national economy. For example,
the states of Oregon and Washington report that ports in the Columbia River employ
2.6 million people and that more than 30% of the wheat exported from the United
States is shipped from these ports.4 According to the management conference for
Corpus Christi Bay, the tourism industry has grown substantially in recent years, and
from 1989 to 1993, tourism expenditures in the bay area increased 41% and related
jobs by 26%.5 Additionally, land development in response to the needs of rapidly
growing populations has expanded the local economies of many estuaries in the
National Estuary Program.

Coastal populations depend on water drawn from an estuary’s freshwater
tributaries to support public infrastructure such as drinking water and water supplies
for industrial facilities, wastewater treatment plants, and irrigation. For example, the
San Francisco Estuary Project, a state agency, estimates that San Francisco Bay’s
freshwater tributaries supply 55% of California’s managed water supply and 40% of
its drinking water for residents of San Francisco, East Bay cities, Stockton,
Sacramento, and southern California.6 Diverted freshwater also has helped to turn the
semi-arid land of central California into a productive agricultural area.
Estuaries provide recreation for coastal residents and visitors, and the state of
Connecticut reports that recreation alone exceeds all others uses in Long Island
Sound.7 Beaches attract swimmers, surfers, and sunbathers, and the management
conference for Santa Monica Bay estimates that 45 million people visit the bay’s 22
3 CRS contacted the program director of each estuary in the National Estuary Program to
compile data on the status of the program, and selected 11 estuaries for inclusion in this report
to provide a balanced geographic representation of the nation’s coastline.
4 Office of the Governor. States of Oregon and Washington. The Nomination of the Lower
Columbia River to the National Estuary Program. January 1995. p. 2-16.
5 Corpus Christi Bay National Estuary Program. Coastal Bend Bays and Estuaries: The
Changing Face of a Landscape. September 1996. p. 18.
6 San Francisco Estuary Project. Sacramento/San Joaquin Delta. September 1995. p. 2.
7 University of Connecticut Cooperative Extension System and Connecticut Sea Grant College
Program. Sea Grant Marine Advisory Program. Sound Values Fact Sheet.

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public beaches each year.8 Many estuaries in the National Estuary program provide
habitat for migratory birds, offering unique opportunities for birdwatchers. In
addition, sport fishing and boating are popular activities at every estuary.
How Does the National Estuary Program Function?
Congress established the National Estuary Program in Section 320 of the Clean
Water Act. This section of the law discusses the scope and administration of the
program, criteria for admitting an estuary, federal programs to gather coastal water
quality data, and grants for developing and implementing comprehensive management
plans to restore and protect water quality. State governors can nominate any estuary
lying entirely or partially within their states to be included in the National Estuary
Program. The nomination must describe why EPA should admit the estuary into the
program, propose a management conference to develop a plan for restoring and
protecting water quality, indicate the likelihood of the plan’s success (including
possible sources of funding), and explain the estuary’s national significance. Factors
that determine whether an estuary is nationally significant include its geographic
scope, the economic and social value of its uses to the nation, and whether its
environmental problems are of national concern. EPA can accept the nomination if
existing pollution control measures are insufficient to achieve or maintain water
quality necessary for protecting fishery populations and sustaining public uses.9
To date, EPA has admitted a total of 28 estuaries that state governors have
nominated for inclusion in the National Estuary Program. Congress granted priority
consideration to 16 of these estuaries, and EPA has included 12 others that also meet
the necessary criteria discussed above. The Estuaries and Clean Waters Act of 2000
(P.L. 106-457) amended Section 320 of the Clean Water Act to award priority
consideration to the Lake Pontchartrain Basin in Louisiana and Mississippi. While
this estuary has not been formally admitted into the National Estuary Program to date,
it will likely be included in the future since EPA has admitted each estuary to which
Congress has granted priority consideration.
Once an estuary is admitted into the program, a management conference
characterizes the environmental problems and develops a Comprehensive
Conservation and Management Plan to restore and protect water quality. These plans
are subject to EPA’s approval prior to implementation. Management conferences
represent diverse interests including: EPA and other federal agencies, state and local
governments, non-profit institutions, industry, and citizens. Management conferences
use water quality data from federal, state, and local agencies to develop their
management plans. Each conference forms a Science and Technical Advisory
Committee to recommend new research if existing data is insufficient to characterize
8 Santa Monica Bay Restoration Project. Summary of the Bay Restoration Plan. December
1994. p. 12.
9 While water quality is poor enough to warrant corrective actions in nearly every estuary in
the National Estuary Program, Charlotte Harbor on the Gulf of Mexico is relatively free of
pollution. EPA admitted it primarily for the purpose of preservation to develop measures that
would prevent environmental problems before they occur.

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environmental problems. The Clean Water Act requires management conferences to
complete their plans within 5 years, but EPA can extend this deadline if the
environmental problems warrant it. A state agency usually coordinates
implementation.
The Clean Water Act authorizes EPA to award grants that match up to 75% of
the costs to develop an estuary’s management plan, and the remaining 25% must
come from non-federal sources. Grants were not originally authorized for
implementation projects since the initial focus of the program was on providing
federal assistance to state and local governments so that they could design their own
plans to restore water quality and develop tailored solutions, rather than rely on
federal regulation for corrective action. However, in response to concerns expressed
by various stakeholders that full implementation of each estuary’s management plan
would not be possible without additional federal assistance, Congress amended
Section 320 of the Clean Water Act under P.L. 106-457 to allow the use of grants for
implementation. While grants for developing an estuary’s management plan may
cover up to 75% of a project’s cost, grants for implementation projects must not
exceed 50% of the cost, and the other 50% must come from non-federal sources.
Apart from National Estuary Program grants, there are three potential sources
of federal funding that are available for implementation. First, capitalization grants
under Section 319 of the Clean Water Act may be used for controlling nonpoint
source pollution in navigable waters where existing measures are insufficient to
achieve or maintain federal water quality standards. Second, states receive federal
funds to develop Water Pollution Control State Revolving Funds, which may be used
to implement applicable measures under an estuary’s management plan. However,
these funds are loans that the recipient must repay to the state. Third, P.L. 106-457
authorized a total of $275 million from FY2001 to FY2005 in matching funds for a
new estuary habitat restoration program to be carried out by the Army Corps of
Engineers, which has the goal of restoring 1 million acres of estuary habitat by 2010.
However, the funding levels for this new program are authorized amounts, which still
must be appropriated by Congress before they would become available. Despite the
availability of these potential sources, federal funding for implementation is limited.
Consequently, the long-term success of each estuary’s management plan will depend
on the commitment and financial resources of the stakeholders. Table 1, below, lists
each estuary in the National Estuary Program and indicates the status of its
comprehensive management plan.
Table 1. Status of the National Estuary Program as of January 2001
Estuary
State
Entry
Plan Status
Puget Sound a, b
Washington
1987
Implementation
Buzzards Bay a, b
Massachusetts
1987
Implementation
Narragansett Bay a, b
Rhode Island
1987
Implementation
Long Island Sound a, b
Connecticut, New York
1987
Implementation
Albemarle-Pamlico Sound a, b
North Carolina
1987
Implementation
San Francisco Bay a, b
California
1987
Implementation

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Estuary
State
Entry
Plan Status
New York-New Jersey Harbor a
New York, New Jersey
1988
Implementation
Delaware Inland Bays a
Delaware
1988
Implementation
Santa Monica Bay a
California
1988
Implementation
Sarasota Bay a
Florida
1988
Implementation
Galveston Bay a
Texas
1988
Implementation
Delaware Estuary a
Delaware, Pennsylvania, New Jersey
1988
Implementation
Casco Bay
Maine
1990
Implementation
Massachusetts Bays a
Massachusetts
1990
Implementation
Indian River Lagoon a
Florida
1990
Implementation
Tampa Bay
Florida
1990
Implementation
Barataria-Terrebonne Complex a
Louisiana
1990
Implementation
Corpus Christi Bay
Texas
1993
Implementation
Peconic Bay a
New York
1993
Development
San Juan Bay
Puerto Rico
1993
Implementation
Tillamook Bay
Oregon
1993
Implementation
New Hampshire Estuaries
New Hampshire
1995
Development
Barnegat Bay
New Jersey
1995
Pending
Maryland Coastal Bays c
Maryland
1995
Implementation
Charlotte Harbor
Florida
1995
Pending
Mobile Bay
Alabama
1995
Development
Morro Bay
California
1995
Pending
Lower Columbia River
Oregon, Washington
1995
Implementation
a Congress awarded priority consideration to these estuaries under section 320 of the Clean Water Act.
b EPA and NOAA studied water quality in these estuaries from 1985 to 1987.
c The Maryland Coastal Bays program does not include the Chesapeake Bay. Under section 117 of the Clean Water
Act, EPA administers a separate federal program to address its environmental problems.
Prepared by the Congressional Research Service with data from the Environmental Protection Agency.
Appropriations
Under the Clean Water Act Amendments of 1987, Congress originally
authorized appropriations of $12 million annually from FY1987 to FY1991 to
administer the National Estuary Program, award grants to develop estuary
management plans, monitor their implementation, and support estuarine research.
P.L. 106-457 reauthorized the National Estuary Program at $35 million annually from
FY2001 to FY2005, and as discussed earlier on page 4, authorized the use of grants
for implementing estuary management plans in addition to developing them.
However, this annual funding level of $35 million is only an authorized amount, and
still must be appropriated by Congress before it would become available. As indicated
in Figure 1 on the following page, Congress has appropriated a total of $217 million
for National Estuary Program grants from FY1987 to FY2001. Annual
appropriations have ranged from an initial level of $11.1 million in FY1987 to $17.9
million in FY1992. The current funding level for FY2001 is $13.8 million, the same
amount as enacted for FY2000.

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Figure 1. National Estuary Program Grant Funding: FY1987 to FY2001
Total Enacted Appropriations: FY1987 to FY2001 = $217 million
Millions of Dollars
17.9
20.0
16.3
16.3
15.7
15.7
15.2
14.4
14.4
13.8
13.8
13.3
13.4
15.0
12.7
13.0
11.1
10.0
5.0
0.0
1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
Amounts indicate extramural funding for National Estuary Program grants and do not include agency
intramural funding for personnel and administrative costs.
Prepared by the Congressional Research Service with data from the Environmental Protection Agency.
What Are the Common Environmental Problems?
While geographic and demographic factors differ among estuaries in the National
Estuary Program, many of them share the following environmental problems:
eutrophication, contamination from toxic substances and pathogens, habitat loss,
altered freshwater inflows, and endangered and non-native species. Common sources
of these problems include releases of pollutants from industrial facilities and
wastewater treatment plants, runoff from stormwater and agricultural land, and
discharges of waste from boaters and swimmers. Developing land and diverting
freshwater also can alter habitats and potentially threaten fishery and wildlife
populations.
Eutrophication
Eutrophication is a process in which excessive plant growth on the water’s
surface lowers oxygen levels and prevents sunlight from penetrating the water, which
can threaten fishery populations and their habitat. Fertilizers and inadequately treated
sewage often contain phosphorous and nitrogen that can act as nutrients to stimulate
excessive plant growth. Runoff from the land and overflows from wastewater
treatment plants can release nutrients into waterways. Eutrophication threatens water
quality in many estuaries. For example, the management conference for Maryland’s
coastal bays reports that eutrophication is the most pervasive environmental problem
facing the estuary and that it is most severe in areas where discharges of nutrients
from agricultural runoff and malfunctioning septic systems are extensive.10
10 Maryland Coastal Bays Program. Management Conference Agreement. June 1996. p. 4.

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Toxic Substances
Toxic substances can cause disease in wildlife and damage their habitat, and
consuming contaminated water or fish can pose a risk to public health. While
industrial facilities are a potential source of toxic substances, other sources are less
direct and more difficult to control, including runoff from stormwater and agricultural
land and overflows from wastewater treatment plants. Toxic substances have been
a persistent problem in Puget Sound, and many areas within its watershed are listed
in the federal Superfund program to clean up hazardous waste sites.11 Rainwater also
is a potential source of toxic substances, as it can deposit air pollution directly into
bays, rivers, and streams. For example, the management conference for Santa Monica
Bay claims that air pollution from the Los Angeles area contributes to the level of
contaminants in the bay and that restoring water quality may depend on continuing
efforts to reduce air pollution.12 Even if current releases of toxic substances were
eliminated, sediments contaminated from historic discharges could continue to
threaten water quality in many estuaries. According to the management conference
for Narragansett Bay, toxic substances released from manufacturing industries 20
years ago continue to degrade the estuary’s water quality today.13
Pathogens
Pathogens are bacteria, viruses, and parasites that can cause numerous human
illnesses. Discharges of inadequately treated sewage from wastewater treatment
plants and septic systems, agricultural runoff from land with farm animals, and
releases of human waste from boaters and swimmers are potential sources of
pathogens. To protect public health, states have periodically prohibited commercial
fishing and closed beaches due to contaminated water at many of the estuaries in the
National Estuary Program. During recent years, the state of Maryland has closed
many areas of its coastal bays to commercial shell fishing due to detecting unsafe
levels of fecal bacteria.14
Habitat Loss
Pollution, land development, and dredging operations to construct and maintain
navigable waterways can deplete or significantly alter habitats, and depletion of
wetlands is a common habitat problem facing many estuaries in the National Estuary
Program. Loss of wetlands can restrict water circulation and lead to higher
concentrations of pathogens, nutrients, toxic substances, and other pollutants.
According to the management conference for Sarasota Bay, land development has
altered 78% of the bay’s native shoreline over the past 40 years, and sediments
11 Puget Sound Water Quality Authority. 1994 Puget Sound Water Quality Management
Plan. May 1994. p. 2-4.
12 Santa Monica Bay Restoration Project. Summary of the Bay Restoration Plan. December
1994. p. 30.
13 Narragansett Bay Project. 1995 Biennial Report. p. 4.
14 Maryland Coastal Bays Program. Management Conference Agreement. June 1996. p. 5.

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deposited from dredging operations during the 1950s and 1960s continue to cause
habitat problems today.15
Altered Freshwater Inflows
Diverting freshwater from an estuary to provide public drinking water and
maintain water supplies for irrigation, wastewater treatment plants, and industrial
facilities can alter the water’s salinity. If salinity rises above certain levels, aquatic
populations that once thrived may no longer be able to survive in the saltier water.
The management conference for Corpus Christi Bay reports that rapid population
growth has increased the demand on public water supplies that depend on the bay’s
freshwater tributaries.16 Recent droughts in Texas have prompted debate over the
increased need for diverting freshwater for human uses while attempting to preserve
water quality.
Endangered Species
Many estuaries in the National Estuary Program provide necessary habitat for
endangered species of animals and plants, and the management conferences consider
measures to protect them when developing their plans. The states of Oregon and
Washington report that the Columbia River historically has had the largest spawning
runs of many salmon species in the world.17 However, these runs have greatly
declined during the past 40 years, and spring and summer runs of chinook salmon in
portions of the river are listed as endangered. The management conference for the
Columbia River is in the process of developing its management plan and intends to
include measures that would restore these fish runs.
Non-Native Species
Species of fish, other wildlife, and plants that are not native to an estuary can
threaten native species by competing with them for habitat and elements in the food
chain. Non-native species can enter an estuary when ships arriving from other
geographic areas discharge ballast water from their hulls. For example, the San
Francisco Estuary Project reports that an Asian clam in San Francisco Bay has
multiplied from a few specimens found in 1986 to populations of 30,000 per square
meter. The project estimates that this one species may have consumed enough of the
bay’s plankton to alter the balance of the food chain and potentially threaten native
species that depend on the same resources.18
15 Sarasota Bay Project. State of the Bay Report. January 1990. p. 18-23.
16 Corpus Christi Bay National Estuary Program. Priority Problems List: Fact Sheet.
17 Office of the Governor. States of Oregon and Washington. The Nomination of the Lower
Columbia River to the National Estuary Program. January 1995. p. 2-12 - 2-15.
18 San Francisco Estuary Project. San Francisco Bay-Delta Estuary. December 1993. p. 4.

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What Has the National Estuary Program Accomplished?
As indicated in Table 1 on page 4, EPA has approved the management plans for
22 of the 28 estuaries in the National Estuary Program. The management
conferences for these estuaries have taken numerous actions to address the
environmental problems discussed above and are following the watershed approach
of managing water resources according to local needs. While this approach offers
greater flexibility, achieving results can require significantly more time than instituting
conventional regulatory measures. For example, public education is an integral part
of most management plans, but convincing individuals to alter behavior that threatens
water quality is an extensive and ongoing process. Since the National Estuary
Program is a collaborative effort, its long-term success depends on the continued
participation, commitment, and resources of each stakeholder. The following sections
of this report provide examples of priority problems and corrective actions to restore
and protect water quality in four estuaries that have been part of the National Estuary
Program since its beginning in 1988: Puget Sound, San Francisco Bay, Albemarle-
Pamlico Sound, and Long Island Sound.
Puget Sound
In 1991, Puget Sound became the first estuary in the National Estuary Program
to have an approved management plan. The Puget Sound Water Quality Action Team,
a state agency under the Office of the Governor of Washington, is coordinating its
implementation, and the Administrator of EPA’s Region 10 serves on the team as a
non-voting member.19 Examples of priority problems and corrective actions include:
reducing pollution from stormwater runoff, restoring habitats, monitoring water
quality, and involving and educating the public.
Reducing Pollution from Stormwater Runoff. The state of Washington
provides technical assistance to local governments for developing stormwater
management programs.20 Some municipalities have developed methods to treat
stormwater runoff more effectively, and many businesses have implemented a variety
of best management practices to treat and decrease runoff from their properties.
Runoff from highways is difficult to control, and the Puget Sound Water Quality
Action Team is coordinating a program to manage this potential source of pollutants,
including oil, grease, and petroleum-based fuels.
Restoring Habitats. The Puget Sound Water Quality Action Team reports that
land development around the estuary has altered critical habitats for many species of
spawning fish and that improperly designed or maintained road crossings block
roughly 3,000 miles of spawning habitats.21 The Washington Department of Fish and
Wildlife is addressing this problem by providing technical assistance to local
19 Puget Sound Water Quality Action Team. Puget Sound Water Quality Work Plan: 1997-
1999. January 1997. p. 1-5.
20 Ibid., p. 94.
21 Ibid., p. 42.

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governments for identifying road crossings that block fish from swimming upstream,
restoring fish passages, and training volunteers.
Monitoring Water Quality. The U.S. Fish and Wildlife Service and the
Washington Departments of Ecology, Fish and Wildlife, Health, and Natural
Resources operate the Puget Sound Ambient Monitoring Program.22 These agencies
are responsible for monitoring different sets of water quality data so that they do not
duplicate their efforts. The monitoring program provides a comprehensive view of
environmental problems across the entire estuary.
Involving and Educating the Public. The state of Washington’s Public
Involvement and Education Fund supports efforts that inform citizens and industry
about the environmental problems in Puget Sound and foster uses that do not threaten
water quality.23 The fund has awarded more than $4 million in grants for 280 projects
that involved nearly 3 million people. For example, the Bainbridge Island School
District has received a grant from the fund to operate a program in which students and
teachers would be trained to monitor water quality in Bainbridge Island’s streams and
watersheds.24
San Francisco Bay
EPA approved the management plan for San Francisco Bay in 1993. The San
Francisco Estuary Project, a state agency under the California Water Resources
Control Board, is coordinating its implementation. Examples of priority problems and
corrective actions include: restoring wetlands, managing water supplies, disposing of
sediments, and monitoring water quality.25
Restoring Wetlands. Some of the actions recommended in the management
plan to restore and protect wetlands are complete. The Bay Area Wetlands
Ecosystem Goals Project is conducting a scientific study that would determine the
types and quantities of wetlands necessary to sustain the estuary’s health, and the San
Francisco Estuary Project reports that it has supported the restoration or enhancement
of over 8,000 acres of wetlands. In addition, the state of California has adopted a no-
net-loss policy for land development affecting wetlands, and the state’s San Francisco
Bay Conservation and Development Commission has hired additional staff to monitor
illegal activities that fill in wetlands.
Managing Water Supplies. In 1995, the U.S. Bureau of Reclamation and 15
local water agencies in the San Francisco Bay area collaborated to conduct the
Central California Water Recycling Project, which studied opportunities for water
recycling on a regional basis. The study estimated that 650,000 acre feet of water
could be recycled each year by 2020. Many municipalities have begun to operate
22 Ibid., p. 55.
23 Ibid., p. 61.
24 Puget Sound Water Quality Action Team home page [http://www.wa.gov/puget_sound]
25 San Francisco Estuary Project. Comprehensive Conservation and Management Plan for
the Bay-Delta: Implementation Progress 1993-1996. October 1996. p. 1-5.

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water recycling programs and are currently recycling 90,000 acre feet of water
annually. Also, the California Department of Water Resources and the U.S. Bureau
of Reclamation are jointly funding a project to research irrigation practices that would
promote greater efficiency in agricultural uses of water supplies.
Disposing of Sediments. The Long Term Management Strategy (LTMS) for
disposing of dredged materials, a private/public cooperative effort, has released a draft
report that proposes options for disposing of sediments over the next 50 years. This
report fulfills an element of the management plan that recommends the development
of such options to address problems with accumulated sediments in San Francisco
Bay. The LTMS has assessed future dredging needs, developed ways to reduce
unnecessary dredging, examined federal and state policies for consistency, and
identified 17 sites where sediments could be reused. Since the LTMS is a
public/private endeavor, the pursuit of these disposal options will depend on the
commitment and resources of the strategy’s developers. In addition, state regulatory
measures have helped to increase the reuse of dredged material for wetlands
restoration, landfill cover, beach enhancement, and road construction.
Monitoring Water Quality. The San Francisco Estuary Institute, a state
agency under the California Water Resources Control Board, administers the Regional
Monitoring Program (RMP) to collect data on pollutants, water quality, human uses,
and aquatic populations. The RMP has tracked trace substances in San Francisco Bay
and its tributaries for the past 4 years to help scientists accurately identify continuing
pollution problems. At the federal level, NOAA is monitoring the effect of diverting
freshwater on salinity levels.
Albemarle-Pamlico Sound
EPA approved the management plan for Albemarle-Pamlico Sound in November
1994. The Division of Water Quality (DWQ) in North Carolina’s Department of
Environment, Health, and Natural Resources is coordinating its implementation.26
Examples of priority problems and corrective actions include: setting daily limits on
discharges of pollutants, controlling agricultural runoff, managing wastewater, and
restoring habitats.
Setting Daily Limits on Discharges of Pollutants. The DWQ has established
total maximum daily loads (TMDLs) that specify the amount of pollution that can
enter Albemarle-Pamlico Sound without threatening water quality.27 The DWQ
completes a TMDL for each industrial facility and wastewater treatment plant before
granting a water discharge permit. As of August 1996, the DWQ had completed
approximately 2,000 TMDLs in the process of awarding these permits. The DWQ
also has developed a water quality management plan that establishes TMDLs for each
river basin draining into the estuary.
26 North Carolina Department of Environment, Health, and Natural Resources. Division of
Water Quality. Implementation of the Comprehensive Conservation and Management Plan:
Summary Report. August 1996. p. i.
27 Ibid., p. 2-3.

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Controlling Agricultural Runoff. The North Carolina General Assembly has
expanded the state’s Agriculture Cost Share Program to offer greater economic
incentives to farmers for controlling pollution from agricultural runoff.28 The
Assembly has increased funding for the Neuse River basin by $1,750,000 and
provided an additional $5,750,000 for the remaining river basins. The state also has
hired additional personnel to provide farmers with technical assistance in developing
measures to reduce pollution in runoff from their lands.
Managing Wastewater. The DWQ has increased its coordination with the
state’s Office of Waste Reduction (OWR) to lower pollution discharged from
industrial facilities and municipal wastewater treatment plants.29 The OWR’s
Prevention Program provides technical assistance to industry, and the Pretreatment
Program assists municipalities in controlling their wastewater more effectively. Both
programs are voluntary and seek to encourage prevention and pretreatment at
facilities and plants that are experiencing difficulty in complying with state water
quality standards. All of North Carolina’s major municipal wastewater treatment
plants are currently participating in the Pretreatment Program.
Restoring Habitats. Federal and state agencies are collaborating to restore
habitats necessary for protecting fishery and other wildlife populations in Albemarle-
Pamlico Sound. The DWQ is coordinating a project funded by a federal grant from
NOAA’s Coastal America program to remove two dams on the Neuse River in
Wayne County, North Carolina.30 The state claims that these dams have interrupted
the free-flowing character of the river and prevented anadromous fish from migrating
upstream during their spawning season. Removing the dams would reopen spawning
habitats on 140 miles of upriver streams.
Long Island Sound
EPA approved the management plan for Long Island Sound in September 1994,
and the Long Island Sound Study is coordinating its implementation. The study is a
joint effort between the states of Connecticut and New York and EPA’s Regions 1
and 2. Examples of priority problems and corrective actions include: lowering inputs
of nitrogen, reducing pathogens, managing toxic substances, and cleaning up floating
debris.31
Lowering Inputs of Nitrogen. The management plan for Long Island Sound
identified eutrophication due to excessive levels of nitrogen as one of the estuary’s
most threatening water quality problems and recommended freezing inputs of nitrogen
at 1990 levels to prevent further water quality degradation. Improvements in treating
wastewater and preventing overflows at many plants have reduced daily nitrogen
loads by 5,000 pounds below what they were in 1990. All of the sewage treatment
plants in Connecticut and Westchester, Nassau, and Suffolk Counties in New York
28 Ibid., p. 8.
29 Ibid., p. 17.
30 Ibid., p. 30-31.
31 Long Island Sound Study. Putting the Plan in Motion. 4 p.

CRS-13
have achieved “no net increases” in nitrogen levels, and other plants are in the process
of making improvements. At the state level, Connecticut and New York have
increased funding for projects that lower releases of nitrogen into the sound.
Reducing Pathogens. The states of Connecticut and New York have prohibited
commercial shellfishing in some areas of Long Island Sound and closed many of the
beaches due to public health risks from pathogen contamination. In Connecticut, the
cities of Bridgeport, New Haven, Middletown, and Hartford have begun long-term
projects to prevent releases of pathogens from combined sewer overflows, and New
York City’s comprehensive sewer abatement program is scheduled for completion in
2006. The states of Connecticut and New York are developing programs to educate
boaters and swimmers about the health risks associated with discharging human waste
into waterways, and numerous marinas are planning to construct new or renovate
existing pump out facilities for boaters to dispose of wastes safely.
Managing Toxic Substances. The state of Connecticut has funded research to
assess the level of toxic substances in Long Island Sound and recommend restorative
actions to reduce their impacts on water quality. The state also has completed
pollution prevention site assessments at 33 industrial facilities and recommended
measures to reduce discharges of toxic substances. One program to pre-treat
industrial wastewater before it is discharged has helped to reduce the amount of
metals released into Long Island Sound by 1,000 pounds per day. In addition, a
toxicity survey of 20 harbors and bays is complete and will be used to develop
effective ways to manage sediments contaminated with toxic substances.
Cleaning Up Floating Debris. According to the Long Island Sound Study,
discharges from combined sewer overflows and stormwater drains are responsible for
a large portion of floating trash and other debris across the estuary. To raise public
awareness about pathways through which trash can enter local waterways, over
16,000 storm drains are painted with an environmental warning, Don’t
Dump—Drains into Long Island Sound, and in New York alone, over 3,000 storm
drains are painted with a bilingual environmental warning in English and Spanish,
Clean Streets—Clean Beaches. In 1995, nearly 900 volunteers removed over 7,000
pounds of trash from 30 miles of shoreline in New York, and over 700 volunteers
removed over 4,000 pounds of trash from 23 miles of shoreline in Connecticut.
Conclusion
The majority of federal programs to protect water quality rely on conventional
regulatory measures that control specific sources of pollution uniformly on a national
level. However, the National Estuary Program departs from this traditional strategy
to control pollution through incorporating a watershed approach in which all affected
interests participate in tailoring solutions to environmental problems for a specific
geographic area. This approach can offer greater opportunities for state and local
governments, industry, and citizens to participate in addressing the environmental
problems that directly affect their communities and can provide increased flexibility
in deciding which measures are better suited for their localities. However, developing
solutions collaboratively can require significantly more time than instituting

CRS-14
conventional regulatory measures, and the financial resources to implement
collaborative solutions depend on the availability of funds from a multitude of public
and private sources.
To date, EPA has approved the management plans for 22 of the 28 estuaries in
the National Estuary Program. While they have taken numerous actions to address
the priority problems identified in their management plans, some of the most common
sources of pollution are indirect and difficult to control, including runoff from
agricultural land and urban streets, overflows from wastewater treatment plants, air
pollution deposited into waterways by rainfall, and releases of waste from boaters and
swimmers. Under the National Estuary Program’s collaborative approach, reducing
pollution from these diffuse sources depends in part on whether coastal populations
are committed to altering established patterns of land use, management of water
supplies, and individual behavior to solve environmental problems in their
communities. So far, the National Estuary Program has made progress in educating
the public about environmental problems, fostering better management of water
resources, reducing pollution, and restoring habitats at certain estuaries. However,
the long-term success of the program depends on the continued commitment,
participation, and resources of the stakeholders in each locality.
Selected References
Clean Water Act Reauthorization. by (name redacted). CRS Issue Brief IB10001.
Updated regularly.
Environmental Protection Agency. National Estuary Program Home Page.
[http://www.epa.gov/nep].
Wetland Issues. by (name redacted) and (name redacted). CRS Issue Brief IB97014.
Updated regularly.

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