How the National Estuary Programs Address — Habitat Loss and Degradation

High-quality habitats are critical for the health of marine and estuarine systems and the human economies that depend on them. Such habitats provide the following essentials for coastal and marine wildlife:

  • Food
  • Cover
  • Migratory corridors
  • Breeding/nursery areas

For humans, healthy coastal habitats attract tourism revenues and seafood industries that are vital to many local economies. These habitats also make coastal areas more resilient to storms and sea level rise. As coastal populations increase, coastal habitats are converted due to the following activities:

  • Development
  • Highway construction
  • Diking
  • Dredging
  • Filling
  • Bulk heading
  • Other activities that degrade coastal ecosystems

When these natural resources are imperiled, so too are the livelihoods of those who live and work in estuarine watersheds.

NEP Approach/Success Stories

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Albemarle-Pamlico National Estuary Program (APNEP)

Submerged aquatic vegetation (SAV) is a critical resource for aquatic life because it:

  • produces dissolved oxygen that fish need to survive;
  • filters pollution; and
  • serves as a food source, hiding place and home for fish, shellfish and crustaceans.

In fact, SAV is valued at about $12,000 per acre per year because of its importance to overall aquatic health and fisheries. In North Carolina, SAV plays an important role in the state's $1.75 billion fishing industry, which employs 24,000 people.

To help protect coastal environments and fishing industries in North Carolina and Virginia, APNEP led a state-federal effort that mapped 138,741 acres of SAV in the Albemarle-Pamlico estuary, which spans southeastern Virginia and northeastern North Carolina. The map provides initial baseline information about the location, quantity and quality of underwater grasses along the coastline.

This information helps planners take steps to avoid development impacts on vulnerable, valuable SAV acreage. The baseline map also enables scientists for the first time to assess pollution level trends in North Carolina and Virginia coastal waters and evaluate coastal conservation efforts.

To map the SAV, airplanes with special cameras flew 1,795 miles along the estuarine coastline during a two-year period. Wind, waves, high humidity and sediment-laden water from rainfall sometimes interfered with the ability to photograph the SAV. So, volunteers sampled the water for clarity to ensure conditions were right for the high-altitude flights. Boat crews with underwater cameras also confirmed the accuracy of SAV locations.

The APNEP continues to work with state, federal, university and non-profit partners to establish an ongoing monitoring program through the North Carolina SAV Partnership.

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Barataria-Terrebonne National Estuary Program (BTNEP)

Grand Isle is Louisiana’s biggest and only inhabited barrier island. The forests, back barrier marshes and sandy beaches of Grand Isle are considered one of the premiere birding destinations in North America. Restoration efforts in the area aim to restore and enhance bird habitat on the barrier island, which is part of the Mississippi Flyway.

For example, BTNEP partnered with The Nature Conservancy for an Arbor Day tree giveaway in Grand Isle. The team planted over 100 trees in the yards of homeowners.

The BTNEP also constructed a shade house at the Nicholls State University Farm to grow out woody species beneficial to Neotropical songbirds that utilize the Mississippi Flyway. The group collected seeds from trees around the state that are suitable for growing in coastal restoration sites with highly disturbed soils with high salinity and pH values. The team worked to establish these species on a man-made ridge in Fourchon and Grand Isle.

Through the multiyear Maritime Forest Ridge and Marsh Restoration Project, BTNEP and partner organizations seek to establish a chenier ridge and adjacent coastal marsh habitats just north of Port Fourchon. The project involved pumping earthen material via hydraulic dredge into shallow open water. The second leg of the project established a ridge with sloping sides and flanking marsh habitats. Volunteers worked to establish these sites by planting native herbaceous grasses and woody plants.

The unparalleled disappearance of Louisiana’s coast can only be surmounted by large-scale projects accomplished through partnerships that bring together the knowledge and resources necessary to address this overwhelming crisis.

Coastal Bend Bays and Estuaries Program (CBBEP)

One of CBBEP's highest priorities is the protection and restoration of habitat for critical species. The CBBEP has an intensive focus on the purchase of major land parcels that provide increased high-quality acreage for waterbird nesting and shorebird habitat.

Galveston Bay Estuary Program (GBEP)

The GBEP’s habitat conservation partnership plans and executes expansive habitat restoration efforts. Since 2000, GBEP and partners have created, protected and enhanced over 20,585 acres of important coastal habitats, leveraging $78 million in local, industry, state and federal contributions. The GBEP operates its programs through a committee structure, and involves federal sources, such as the U.S. Fish and Wildlife Service and Coastal Impact Assistance Program, in its annual habitat conservation planning process.

Maryland Coastal Bays Program (MCBP)

The MCBP and its partners reclaimed a sand mine by converting its 32-acres into an Atlantic white cedar wetland, a once very common ecological habitat type which is now virtually non-existent in Maryland. Restoration projects like this provide a variety of benefits.

A creek running through the Lizard Hill Wetland Restoration project area had consistently high levels of nitrogen. During restoration, the nutrient-rich runoff from adjacent agricultural fields was routed through the functional wetlands of the project site. This naturally removed nutrients prior to discharge into a tributary of the St. Martin River. Recent water quality data analysis confirms that water leaving the project site carries less nitrogen and phosphorus than water entering the site.

Another part of the restoration included adding grade control structures which reconnected the stream to its floodplain. This rehydrated the forested floodplain and expanded the drainage area to about 13.5 miles, reducing storm peak flows.

This project also re-established critical habitat for local endangered and uncommon species, such as pitcher plants, swamp pink and Hessel’s hairstreak butterfly. Sundew, an uncommon carnivorous plant, has already been found on the site.

Mobile Bay National Estuary Program (Mobile Bay NEP)

The Mobile Bay NEP (Alabama) partnered with the Baldwin County Commission to prevent on-site erosion and restore wetland, riparian and stream habitat in Magnolia Springs Park. The project was part of the Mobile Bay NEP’s Habitat Incentives Program, which promotes the acquisition and restoration of rare, highly sensitive or high-value sites within the Mobile Bay NEP study area.

Morro Bay National Estuary Program (Morro Bay NEP)

The Morro Bay NEP (located in California) and its partners improved fish passage in streams by removing man-made structures that impeded fish migration upstream. Their work resulted in enhanced access to 6.29 miles of stream for steelhead and other species. Additional habitat protection measures put in place by the program include land conservation purchases and easements.

 While estuaries naturally fill with sediment as part of the geologic process, the rate of sedimentation in Morro Bay (located in California) is as much as ten times the natural rate, due largely to changes caused by people. Moreover, major factors contributing to increased sedimentation in the estuary include:

  • Fires
  • Overgrazing
  • Erosion from development
  • Loss of floodplains

The estuary could lose all of its open-water and inter-tidal habitat within 300 to 400 years. Increased sedimentation also adversely affects plants and animals. Increased sedimentation in the water can bury, or partially block sunlight from reaching, eelgrass beds, destroying these underwater meadows. Sediment also buries and clogs gravel spawning beds for steelhead trout.

The Morro Bay NEP and its partners take a holistic approach to restore the natural sedimentation process by:

  1. Stopping sediment at the source; and
  2. Catching it downstream before it reaches the estuary.

As one measure to stop sediment at the source, the program developed a fire management plan to help local fire districts reduce the risk of large catastrophic fires that leave bare slopes vulnerable to erosion.

The program also teamed with the local Resource Conservation District and ranchers to improve grazing practices and to fence cattle out of creeks, further reducing erosion. To date, approximately 35 percent of stream miles in the watershed have been fenced from cattle.

In another source-control strategy, the program partnered with land owners to improve eroding ranch roads. For example, Camp San Luis Obispo road improvements, funded partially through the program, will prevent an estimated 2,800 cubic yards of soil from entering the nearby creek.

ranch road erosion morro

Further, floodplain restoration efforts help these areas catch sediment before it reaches the estuary. The program and its partners work to restore the expansive historic floodplains diminished by past agriculture practices. One such project, the Chorro Creek Enhancement Project, is estimated to have prevented over 150,000 cubic yards of sediment from reaching the bay.

To date, approximately 300 acres of historic riparian floodplain have been protected or restored. These floodplains not only trap sediment from reaching the bay, but also provide important fish and wildlife habitat.

Through the program's monitoring efforts, staff are working to determine accurate annual sediment loading values for the tributaries in the watershed. The program will use this information to better target areas for project implementation and help refine the current sediment TMDL in the watershed.

San Juan Bay Estuary Program (SJBEP)

In 2008, the SJBEP (located in Puerto Rico) deployed 45 artificial reefs structures in the Condado Lagoon. The effort included the creation of the first underwater interpretative trail in the San Juan Bay Estuary and adjacent watersheds. The structures increased fish diversity by 90 percent. Moreover, approximately 2,500 new coral colonies are growing over the artificial reef surfaces. This project created and enhanced one acre of benthic habitat in the Condado Lagoon.

Santa Monica Bay National Estuary Program (SMBNEP)

In 2013, The Bay Foundation and partners completed the Malibu Lagoon Restoration and Enhancement Project, which restored an impaired wetland. This wetland was on U.S. EPA’s list of impaired water bodies for over a decade due to excess nutrients and low oxygen levels. The Project’s core goals included the following:

  • Improving the ecological health of the lagoon’s system by enhancing habitats for native wildlife
  • Creating several acres of new wetlands
  • Increasing tidal flushing and water circulation to improve water quality and eliminate the “dead zones” and oxygen-deprived areas

Through two years of a five-year monitoring program, the project is on track to meet or exceed the documented criteria for success, with significantly improved water quality and circulation results, and improving condition scores over time. The Lagoon also now functions as nursery habitat for juvenile estuarine fish. Further, there is a shifting trend from a pre-restoration pollution-tolerant benthic invertebrate community to a more diverse, sensitive invertebrate community.

Another notable SMBNEP restoration effort is the Palos Verdes Kelp Forest Restoration Project. This project endeavors to offset the loss of 75 percent of giant kelp communities on the Palos Verdes Peninsula. In the past two years, community volunteers and commercial fishermen spent over 5,500 hours reducing sea urchin densities on the shallow rocky reefs and have restored 33 acres. The teams crushed 1.4 million sea urchins to enable the natural recruitment and regrowth of the giant kelp forest. Once completed, the project could encompass more than 150 acres.

The ecological response has been direct: giant kelp returned to the reefs and formed a canopy, and biomass and the richness of fish species increased. The remaining sea urchins, valuable to the red sea urchin fishery, are recovering quickly and are of value to the fishery, at a modeled benefit of 883 percent for every unit restored.

Sarasota Bay Estuary Program (SBEP)

Since 1993, SBEP (located in Florida) has overseen the completion of nearly 70 habitat restoration projects, with help from partner agencies, conservation groups and volunteers. Between 2014-15, the SBEP and several key partners managed two major wetland restoration projects.

The first project took place at Oscar Sherer Park, an urban state park in southern Sarasota County. This project consisted of the following three unique elements:

  • Restoring the shoreline along Lake Osprey, which lies adjacent to the Park’s Nature Center and gets the concentration of Park visitors.
  • Restoring an isolated wetland and creating new “frog ponds” adjacent to one of the Park’s hiking trails.
  • Rehabilitating Big Lake, an historic borrow pit that needed extensive shoreline and shallow water work to restore habitat for wading birds.

The other major project took place at the FISH Preserve in the Village of Cortez, Manatee County. Acquired for its historically important coastal habitats, this 100-acre parcel saw a lot of abuse over the decades and needed a major restoration. Here, SBEP focused on restoring saltwater wetland and creating improved tidal circulation throughout half of the available upland acreage. The SBEP partnership planted extensive native vegetation along the wetland edges and upland islands.

The SBEP also completed two exciting subtidal habitat projects in the past few years.

In the first project, the SBEP created over four acres of oyster habitat. Completed over three years, the oyster reefs now support thriving fish and invertebrate communities. Moreover, they closely mimic the form and function of nearby natural oyster reefs.

In 2013, the SBEP rejuvenated its artificial reef program within Sarasota Bay and addressed nearly a dozen “bay reefs” that were idle since material was last placed on them in 2004. With the help of Reef Innovations of Sarasota, SBEP designed several new reef modules to attract juvenile gag grouper, which use the bay early in their life cycle.

Also in 2013, the project deployed several dozen modules, including “deep covers,” “Lincoln logs” and “layer cakes,” at three Sarasota County reefs. Subsequent monitoring revealed a variety of pelagic and reef fish, as well as highly economically valuable stone crabs, using these habitats.

The SBEP’s comprehensive study of the Bay’s artificial reefs found up to 30 different species of fish and invertebrates utilizing these structures as habitat.

Tillamook Estuaries Partnership (TEP)

The TEP facilitated 26 partner organizations in the Miami River Wetlands Enhancement project. The results of this 58-acre restoration initiative included:

  • Creating 4,500 feet of new channels
  • Placing 183 pieces of large woody debris
  • Planting 19,000 native species

More than 51 acres were purchased by The Nature Conservancy and set aside as a protected reserve.

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Last updated on July 23, 2024