NATIONAL
ESTUARY
PROGRAM
EFFECTIVE • EFFICIENT • COLLABORATIVE • ADAPTABLE
THE NEP IS EFFECTIVE
For two decades, National Estuary Pro-
grams (NEPs) across the United States
have worked to revive and restore our na-
tion's estuaries—where the rivers meet the
seas. The continued success of the NEP
hinges in part on an unwavering commit-
ment to a core principle: effectiveness.
In efforts to help towns and cities imple-
ment the Clean Water Act (CWA), NEPs
have launched and assisted in wide-rang-
ing actions designed to improve water
quality and address habitat loss and deg-
radation. CWA programs are at work to
address water quality improvements, and
public outreach programs are on course
to help people learn about estuaries and
understand the importance of these ef-
forts. NEPs are also addressing the pol-
lutants that degrade habitat and adversely
impact the living resources that inhabit
those areas.
Here are some examples of how NEP pro-
grams nationwide have championed the
cause to protect, rebuild and restore our
nation's estuaries.
HABITAT RESTORATION
The Barataria-Terrebonne National Estuary in Louisiana—
the 4.2 million acre region between the Atchafalaya and
Mississippi Rivers—is the fastest disappearing landmass
on Earth.
As estuaries and wetlands in the region rapidly turn to
open water, destroying interior vegetative marsh and ridge
habitats, coastal communities are increasingly vulnerable
to storm surge, deprived of potable drinking water, and
face the inevitable exhaustion of resources that supply the
nation with shrimp, oysters, fish, oil, and gas, as well as
recreational opportunities.
NEP IN ACTION
To recover this prized coastal habitat, the Barataria-Terre-
bonne National Estuary Program (BTNEP) and the Greater
Lafourche Port Commission are working cooperatively with
other partners on a three-phase effort designed to restore
a natural ridge that will provide needed protection to fish,
wildlife, and plants. The main component of the Maritime
Forest Ridge and Marsh Restoration Project at Port
Fourchon is the harvesting of river bed sediment, directing
it through pipelines to build new land, and planting new
vegetation—specially selected grass plugs, seeds, and
woody plants that will offer critical protection to habitat in
the region.
The Ridge Project" is supported by grants and gener-
ous donations of time, expertise, and money from birding
EFFECTIVE • EFFICIENT • COLLABORATIVE • ADAPTABLE
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clubs, oil companies, the Federal Natural
Resources Conservation Service, and
other interest groups. When the project is
completed, the region will see 2.25 miles
of restored ridge and marsh habitat—more
than 120 across maritime forest ridge,
marsh, and tidal creeks.
Although the effects of Hurricanes Katrina
and Rita have slowed progress, the 60-
plus acres of new surface area created
during the first phase of the project-
before the hurricanes hit—prevented
damage to the Port and surrounding land
that would have otherwise occurred with-
out the ridge, according to the Greater
Lafourche Port Commission—an outcome
that verifies the effectiveness of BTNEP's
Comprehensive Conservation Management
Plan and the value it brings to the country.
The next 40 acres of the project will be
shaped with tidal channels constructed
every 1,000 feet along the project site to
provide for water exchange between the
mitigated marshes to the south and the
shallow open water areas to the north.
Long-term plans include construction of
new foot paths and board walks, and
observation platforms and bridges along
the ridge and out onto the marsh platform.
Kiosks, interpretive signage and a nature
center will complete the effort.
Their experience will be applied to
future restoration projects in Louisiana and
across the country. The BTNEP is quickly
becoming a major resource for habitat
restoration information as they field daily
inquiries from NEPs across the country,
other watershed management groups, and
environmentalists worldwide.
NUTRIENT REDUCTION
The Long Island Sound Study (LISS) is achieving measur-
able results from their efforts to reduce nitrogen discharg-
es to the Long Island Sound—where sewage treatment
plants discharge more than a billion gallons of treated
effluent, which contains oxygen-demanding material and
nitrogen.
Large inputs of nutrients such as nitrogen have over-fertil-
ized significant areas of the Sound, fueling the excessive
growth of marine plants that deplete the water's oxygen.
These low dissolved oxygen levels—a condition called
hypoxia—degrade the habitat for fish and shellfish.
NEP IN ACTION
To address the problem, the LISS provides progressive
leadership on several efforts, including a push to upgrade
wastewater treatment plants, and to implement watershed
protection measures aimed at reducing polluted runoff.
The LISS also supports emission reduction programs de-
signed to lessen nitrogen deposits from the air.
To gain a better understanding of the relationship between
nitrogen discharges to the Sound and dissolved oxygen
levels, they used scientific information based on a three-
dimensional water quality model that helped them estab-
lish a nitrogen reduction target of 58.5 percent.
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Connecticut and New York incorporated the target into
a Total Maximum Daily Load (TMDL) for nitrogen to help
meet Water Quality Standards. The States have also re-
vised their water quality standards for dissolved oxygen in
marine waters to reflect EPA criteria for protection of living
resources in marine waters and created new provisions
for pollutant trading for cost-effective attainment of Water
Quality Standards. Implementation of the TMDL is moving
forward, with upgrades at wastewater treatment plants
decreasing the amount of nitrogen to Long Island Sound
in 2006 by 52,000 Ibs. per day compared to baseline
levels.
These reductions are partly due to innovative strategies.
Connecticut's Nitrogen Credit Exchange program, which
won a 2007 EPA Blue Ribbon Water Quality Trading
Award, sold 8.5 million worth of credits in four years. By
2006, 35 percent of the 79 participating sewage treat-
ment plants had reduced nitrogen output below assigned
permit limits, making them eligible to sell a total of $1.32
million in nitrogen credits. This innovative program is ex-
pected to save the State between $200 million and $400
million in wastewater treatment construction costs over
the next decade.
In New York, "bubble permits' now provide flexibility to
dischargers on how to attain permit limits—an approach
expected to save New York City up to $660 million in
sewage treatment plant upgrade costs. And the States
of Massachusetts, Vermont, and New Hampshire worked
with the Connecticut River Nitrogen Work Group to dis-
cuss reducing nitrogen loading from the Connecticut
River watershed to the Long Island Sound—a collabora-
tion that led to four years of nitrogen monitoring and new
water quality models to identify sources and quantify
loads of nitrogen from the upland States.
CLEAN WATER ACT - TOTAL
MAXIMUM DAILY LOAD (TMDL)
The goal of the Clean Water Act (CWA) is to
restore and maintain the chemical, physical, and
biological integrity of our nation's waters. Under
Section 303(d) of the CWA, States, territories
and authorized tribes are required to develop
lists of waterbody segments impaired by a pol-
lutant and needing a Total Maximum Daily Load
CTMDL).
A TMDL specifies the maximum amount of a
pollutant a waterbody can receive and still meet
water quality standards. A TMDL is made up
of the sum of all point source loads ("wasteload
allocation') and load associated with nonpoint
sources ("load allocation').
National Estuary Programs develop strategies to
help attain or maintain water quality standards
through mechanisms such as TMDLs.
TOTAL rvVMMUM DALY LOAD
The Hillsborough River, a highly urbanized water-
body located within the City of Tampa, is a signifi-
cant tributary to Tampa Bay. Bacterial contamina-
tion (fecal coliform) from human impacts such as
sanitary sewer overflows, malfunctioning septic
systems, the homeless population, pet waste and
agricultural drainage has impaired the river and
threatened coastal swimming, fishing and shellfish
harvesting.
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As required by Section 303(d) of the Clean Wa-
ter Act, the Tampa Bay Estuary Program (TBEP)
and many partners are working to address the
water quality of the Hillsborough River by devel-
oping an implementation plan to address State
and Federal Total Maximum Daily Load (TMDL)
requirements. TMDLs are measures that specify
the maximum amount of pollutant a waterbody
can receive and still meet water quality stan-
dards.
THE NEP IN ACTION
To implement the TMDL, the TBEP collaborated
with stakeholders to develop a Basin Management
Action Plan (BMAP)—a watershed-based approach
to identify and address water quality impairments in
a major drainage basin in Hillsborough County.
The team reviewed existing water quality informa-
tion; developed an inventory of existing or planned
pollution reduction projects, identified new issues
and information gaps, and developed comprehen-
sive plans to address sources of pollution. A micro-
bial source tracking program was also developed
to help assess the cause of bacterial contamination
in different portions of the river.
The BMAP draft identified three key solutions for their
potential to remove Hillsborough River from the 303(d) list
of impaired waters for bacterial contamination. In addi-
tion BMAP is a viable model for addressing water qual-
ity impairments in other waterbodies of the Tampa Bay
watershed.
The three key actions in the draft BMAP are:
• Installation of auxiliary battery-powered generators
at sanitary sewer pump stations throughout the
City of Tampa to prevent sewer overflows during
power outages;
• Comprehensive, integrated stormwater treatment
planning and implementation; and
• Enhanced educational programming to increase
public awareness of the proper disposal of pet
waste.
TBEP has already made significant gains in awareness
efforts to educate the community about improperly dis-
posed of pet waste and its effect on water quality. Dur-
ing a single pilot project, they were able to effect a 46
percent decrease in waste piles—and the effort is now
under consideration in neighboring counties and cities.
The team—including the Environmental Protection Com-
mission of Hillsborough County; city and county public
works, planning and water departments, health depart-
ments, the Southwest Florida Water Management Dis-
trict, private industries, scientists, and citizens—recently
submitted its draft BMAP to the Florida Department of
Environmental Protection.
CREATING AN ARTIFICIAL REEF
Since the 1950s, the Sarasota Bay system has lost about
4,500 acres of hard bottom habitat due to dredge and fill
activities, adversely impacting the productivity and bio-
diversity of Sarasota Bay's coastal lagoon system. Hard
bottom habitat provides a substrate for soft corals, filter-
ing bivalves and crustaceans, which in turn support a
variety of life stages of game and non-game fin fish as
well as shellfish. Historically these hard bottom habitats
supported a thriving fishing industry along Florida's Gulf
Coast and bay inlets.
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NEP IN ACTION
The Sarasota Bay
Estuary Program (SBEP)
helped to establish an
Artificial Reef Program in
1996 to replenish this
vital habitat type. Since
its inception, the SBEP
and its partners have
deployed approximately
5,000 artificial reef mod-
ules and other materi-
als of opportunity (such
as concrete culverts) in
the waters in and near
Sarasota Bay, targeting
deeper areas and chan-
nel markers.
The $674,000-project is a joint effort funded by
several groups, including Manatee and Sarasota
Counties, Sarasota Sportsmen's Association,
Mote Marine Laboratory, Florida Fish and Wild-
life Commission, and Reef Innovations, which
manufactures the reef balls and offers monitor-
ing assistance. It also features a public outreach
component, with children, parents and teachers
from SBEP-supported groups such as Bay Bud-
dies and Reef Rakers, assisting in reef clean-up
events and artificial reef surveys. This important
project is providing critical habitat for a variety of
marine organisms while giving scientists an op-
portunity to do valuable research on bay bottom
restoration. The reefs also provide more oppor-
tunities to fish in small vessels.
SBEP and its partners placed many of the reef modules
in clusters of various sizes to see what size grouping
of modules produces the optimum habitat for the reef
organisms.
In 2006, Mote Marine Laboratory began a two-year proj-
ect monitoring five of the Sarasota Bay artificial reef sites
for the SBEP. Preliminary results indicate that different
numbers of reef modules support different life stages of
marine organisms and a variety of species. By imple-
menting an innovative artificial reef strategy—young fish
are now living near the new reefs—SBEP is creating a
new kind of habitat, and is increasing the biodiversity of
Sarasota Bay.
During 2002, the SBEP conducted two sea-
sons of sampling on several established artificial
reefs within Sarasota Bay, identifying more than
25 species, including gray snapper, gag grou-
per, sheepshead and stone crab. The research
indicated that a variety of reef types would be
required to increase species diversity. The
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STORMWATER TREATMENT
The Indian River Lagoon National Estuary Program (IRL NEP)
has ambitious goals to improve water and sediment quality
and restore and rehabilitate damaged coastal habitat.
Excessive freshwater discharges into the central and
southern lagoon due to diversion of floodwaters from the
St. Johns River and Lake Okeechobee and pollutant-laden
stormwater into the lagoon have caused fish kills in some
areas of the lagoon along with the loss and/or degradation
of thousands of acres of seagrass, salt marsh and man-
grove wetlands.
NEP IN ACTION
To reverse the damage and save the lagoon, the IRL NEP,
along with numerous local, State and Federal government
agencies including county mosquito control districts, the
U.S. Fish and Wildlife Service, St. Johns and South Florida
Water Management Districts (SFWMD), Canaveral National
Seashore National Park Service and the National Aeronau-
tic and Space Administration (NASA) have joined forces
and funding efforts. As a result, more than 100 stormwater
reduction and treatment projects now exist throughout the
watershed. Stormwater retrofit projects and large stormwa-
ter abatement and detention projects have been implement-
ed or are in the planning stages, including a State-funded
$10-$20 million project to redirect 100 miles of expanded
watershed back to the St. Johns River.
Signs of recovery are already present with respect to
coastal wetland habitat, water clarity, seagrass habitat and
fisheries. The reconnection and rehabilitation of more than
27,000 acres of coastal wetlands and reductions in pollut-
ant loads from constructed storm water treatment projects,
coupled with substantially less rainfall in the last decade,
have helped reduce runoff. This also helps lower inputs of
nitrogen, phosphorus, soils and turbidity.
The IRL NEP goal for wetland rehabilitation is 34,943 acres.
To date, approximately 24,760 acres have been rehabili-
tated in the north central portion of the lagoon and 4,695
acres in the south. The rehabilitation of nearly 30,000
acres, along with a marked increase in seagrass coverage
across these estuary segments and increased landings of
sea trout, pinfish and mangrove snapper, indicate that this
ambitious and fast-acting NEP is effecting change.
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BACTERIAL MONITORING AND
WATER-QUALITY STANDARDS
Tillamook Bay—Oregon's third largest estuary—
supports a thriving commercial and recreational
shellfishing industry. Unfortunately, bacteria
concentrations found in all five of the Bay's ma-
jor tributaries routinely violate State and Federal
water quality standards, threatening human health
and causing commercial harvest area closures.
As is often the case in estuaries across the coun-
try, Tillamook Estuaries Partnership (TEP) knew
bacteria came from a combination of point and
non-point sources including agricultural runoff,
failing septic systems, overloaded municipal treat-
ment plants, and urban stormwater. The tricky
part was identifying exactly where these sources
were delivering the largest loads and quantify-
ing how much bacteria was threatening the Bay's
health.
NEP IN ACTION
With its Comprehensive Conservation and Man-
agement Plan (CCMP) serving as a guide, the
TEP launched an ambitious bacteria research and
monitoring effort in the basin. Data produced
from this effort has allowed TEP to apply mitiga-
tion efforts exactly where they are needed in
order to efficiently and effectively achieve water
quality goals. In addition, bacteria data collected
through TEP's monitoring was also used by the
State of Oregon to create the Tillamook Bay Bac-
teria Total Maximum Daily Load (TMDL).
TEP began its monitoring program in 1996,
launching an extensive Storm-Based Monitoring
Program to identify and evaluate bacterial con-
centrations attributable to the watershed's differ-
ent land uses. The effort also identified suitable
long-term sampling sites for tracking the status
and trends of bacteria throughout specific river
reaches. A small team of dedicated volunteers
joined the effort the following year, and 13,000
samples later, the TEP is reporting significant
progress in 2007.
TEP's trend data has led to some important dis-
coveries, including the determination that forest-
ed areas of the watershed generally meet water
quality standards for bacteria, indicating that
forest wildlife is not a key contributor of bacterial
contamination as some thought. Working with
Oregon State University researchers in 2001, the
TEP began a three-year genetic marker study in
the Tillamook Bay Watershed. The study en-
abled scientists to discriminate among bacteria
from humans and ruminant sources (Ruminant
forces includes cows, elk, and deer). They
found widespread contamination from farm ani-
mal waste in specific segments of the river and
high concentrations of human waste in other
parts. Using the data, watershed managers can
now build the best strategies for decreasing fe-
cal pollution indicators in specific areas.
The TEP is working with agricultural landowners,
including the local dairy cooperative, which made
some important improvements to its discharge
system so that its effluent no longer discharges
directly into the Wilson River. With a credible,
scientific framework the TEP has developed part-
nerships with local municipalities on habitat res-
toration and stormwater management projects.
Additionally, a voluntary educational program tar-
geted to small landowners offers assistance with
septic system upgrades, riparian re-vegetation
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projects, and workshops about the importance
of fencing off riparian areas to prevent livestock
from entering streams and rivers.
While the lower sections of four of the key riv-
ers in the Tillamook Bay watershed still violate
Oregon's water quality standards for recreational
use, the fifth tributary, the Wilson River, has
been in compliance since 2005, and statistically
significant trends indicate that bacteria concen-
trations remain on a steady decline.
More than a decade's worth of status and trend
information is paying off for the TEP with targeted
approaches that support successful, efficient im-
plementation of the Comprehensive Conservation
and Management Plan. Investing in efforts that
strategically target land uses that contribute to
surface water bacteria is bringing the Tillamook
Bay watershed closer to coming into compliance
with State and Federal water quality standards.
REAL RESULTS IN REAL PLACES
The US EPA National Estuary Program (NEP), a
unique and voluntary community-based program
established in 1987 under the Clean Water Act
(CWA) Amendments, works to restore and
maintain the water quality and ecological integrity
of estuaries of national significance.
Through strong commitment, trust, and
significant time and resources spent by many
State, local and Federal partners, the NEPs have
made substantial progress in protecting and
restoring habitat in their estuaries. NEPs have
implemented wide ranging actions to rehabilitate
wetlands, create artificial reefs, and plant
riparian buffers among many other types of
activities that address the loss and degradation of
multiple habitats and estuarine watersheds.
NEPs and their partners have produced real
on-the-ground environmental results—improving
water quality, erosion, flood control, open space, and
creating habitat.
There are 28 NEPs, located in 18 U.S. coastal States
and Puerto Rico, which are designated estuaries of na-
tional significance for their distinct economic, ecological,
recreational, and aesthetic values.
For more information contact:
US EPA
Office of Wetlands, Oceans and Watersheds (OWOW)
Coastal Management Branch
Mail Code 4504T
1200 Pennsylvania Avenue, NW
Washington, DC 20460
Tel: 202.566.1260
Fax: 202.566.1336
www.epa.gov/owow/estuaries
The NEP: Applying the Clean Water Act in
ways that are Effective, Efficient, Adaptable,
and Collaborative.
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