Challenges Facing Our Estuaries

Key Management Issues

See also Managment Approaches to Estuarine Environmental Problems and EPA's research activities.

Introduction to Common Estuarine Environmental Problems

Although each of the estuaries in the National Estuary Program (NEP) is unique, they all face similar environmental problems and challenges: overenrichment of nutrients, pathogen contamination, toxic chemicals, alteration of freshwater inflow, loss of habitat, declines in fish and wildlife, and introduction of invasive species. While no regional or national conclusions can be drawn about the overall health of estuaries in the NEP, these problems tend to cause declines in water quality, living resources, and overall ecosystem health.

These key management issues are common to many coastal watersheds across the country. Therefore, the transfer and exchange of scientific and management information among NEPs and to other coastal watershed managers is critical to ensure success in restoring and protecting the health of our nation's estuaries.

We have seen over the years that the impacts of these problems are quite visible. Pathogens have led to a large number of shellfish bed closures. Over-enrichment of nutrients is contributing to lower dissolved oxygen levels and loss of seagrasses. Introduction of invasive species is adversely affecting native species and their habitats.

The following discussion attempts to provide a brief overview of the most common problems facing the 28 Estuary Programs (NEPs). These problems were identified by over 125 representatives from the NEPs and EPA at a recent workshop co-sponsored by EPA and the Association of National Estuary Program (ANEP). These representative included NEP Directors and staff, scientists, outreach coordinators, citizens, business representatives, local government officials, and EPA. The information provided here is excerpted from papers prepared for workshop discussions. Although many NEPs may be experiencing these common problems, only a few highlights and examples are presented to provide a sense of the issue.

For more information about these common issues, see the National Water Quality Assessments (305b Report). Also see the discussion of Management Approaches to learn how the various NEPs around the country are dealing with the problems discussed below.

To top of page

Nutrient Overloading

Sources and Impacts

Nutrients such as nitrogen and phosphorus are necessary for growth of plants and animals and support a healthy aquatic ecosystem. In excess, however, nutrients can contribute to fish disease, red or brown tide, algae blooms, and low dissolved oxygen. The condition where dissolved oxygen is less than 2 parts per million is referred to as hypoxia. Many species are likely to die below that level- the level of healthy waters is 5 or 6 parts per million. Sources of nutrients include point and non-point sources such as sewage treatment plant discharges, stormwater runoff from lawns and agricultural lands, faulty or leaking septic systems, sediment in runoff, animal wastes, atmospheric deposition originating from power plants or vehicles, and groundwater discharges.

Excessive nutrients stimulate the growth of algae. As the algae die, they decay and rob the water of oxygen. The algae also prevent sunlight from penetrating the water. Fish and shellfish are deprived of oxygen, and underwater seagrasses are deprived of light and are lost. Animals that depend on seagrasses for food or shelter leave the area or die. In addition, the excessive algae growth may result in brown and red tides which have been linked to fish kills, manatee deaths and negative impacts to scallops. Increased algae may also cause foul smells and decreased aesthetic value.

NEP Examples

From mid-July through September of each year, up to half of Long Island Sound experiences dissolved oxygen levels that are insufficient to support healthy populations of marine life. The low dissolved oxygen levels have been tied to to the over-fertilization of the Sound with nitrogen, resulting in the excessive growth of planktonic algae. The blooms sink to the botton and decay, depleting the water of oxygen. The dense algal blooms also cloud the water and shade the bottom, inhibiting the growth of submerged aquatic vegetation- important habitat for shellfish and juvenile finfish.

Certain areas of Narragansett Bay in Rhode Island experience low dissolved oxygen levels in mid- to late summer due to excess nitrogen. Mild to severe hypoxic events have been recorded in four areas. Algal production has approximately doubled since the first European settlers came to Rhode Island, and eelgrass beds have disappeared over most of the Bay.

In Maryland Coastal Bays runoff from land contributes more than 50 percent of nitrogen loadings. Half of these loadings are associated with agricultural feeding operations (primarily poultry), despite the small amount of land area occupied by these operations.

Water quality declines contributed to the loss of nearly half of Tampa Bay's seagrasses- almost 19,000 acres- from the 1950s to the 1980s. However, that trend is beginning to be turned around. The Bay's total annual nitrogen loading in 1976 was more than 2.5 times the average 1992-1994 load of 3,800 tons per year. Seagrasses have gradually returned in areas where water clarity has improved due to reductions in nitrogen loadings from wastewater treatment plants in the late 1970s. However, these gains could be offset by population growth. Nitrogen loading is expected to increase at a rate of 17 tons per year as a result of population growth unless additional actions are taken.

The National Estuary Programs are working to address the problem of nutrient overloading. Click here to learn more about the various management approaches the NEPs are taking towards the nutrient problem.

To top of page

Pathogens

Sources and Impacts

Pathogens are disease-causing organisms such as viruses, bacteria, and parasites. They are found in marine waters and can pose a health threat to swimmers, surfers, divers, and seafood consumers. Fish and filter feeding organisms such as shellfish concentrate pathogens in their tissues and may cause illness in persons consuming them. Pathogen contamination can result in the closure of shellfishing areas and bathing beaches. Sources of pathogens include urban and agricultural runoff, boat and marina waste, faulty or leaky septic systems, sewage treatment plant discharges, combined sewer overflows, recreational vehicles or campers, illegal sewer connections, and waste from pets or wildlife.

NEP Examples
A variety of point and non-point sources of fecal-borne microbial pathogens that contaminate Great Bay and Hampton Harbor Estuaries in New Hampshire have led to closings of clam and oyster beds. In 1985, 71 percent (9,000 of 12,599 acres) of classified shellfish waters were closed to shellfishing in Great Bay Estuary. In 1988, 72 percent of shellfish waters were closed in Great Bay.

Standards for bacterial indicators are exceeded on numerous occasions at certain beaches and piers around the Santa Monica Bay during the summer swimming season. An epidemiological study of swimmers found that there was an increased risk of illness- more than 50 percent higher- for those who swam near flowing storm drains versus those who swam further away. Correlations were also found between incidences of illness and swimming in areas with high densities of bacterial indicators.

In a Phillippi Creek near Sarasota Bay, warning signs have been posted of the potential health risks associated with exposure to creek waters.

Over 2,952 acres of bay bottom are closed to shellfishing either year round or seasonally in Peconic Bay on Long Island. This represents about 14 percent of the productive shellfish areas. Of the 30 public bathing beaches, one has been closed due to bacterial contamination.

The National Estuary Programs are working to address the problem of pathogens. Click here to learn more about the various management approaches the NEPs are taking towards the pathogen problem.

To top of page

Toxic Chemicals

Sources and Impacts

Toxic substances such as metals, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), heavy metals, and pesticides are a concern in the estuarine environment. These substances enter waterways through stormdrains; industrial discharges and runoff from lawns, streets and farmlands; sewage treatment plants; and from atmospheric deposition. Many toxic contaminants are also found in sediments and are resuspended into the environment by dredging and boating activities. Bottom-dwelling organisms are exposed to these chemicals and may pose a risk to human health if consumed. As a result there may be fishery and shellfish bed closures, and consumption advisories.

NEP Examples
Toxic contamination in Massachusetts Bays is most serious along the North Shore and in the vicinity of Boston Harbor where industrial wastewater and urban runoff contain relatively high loadings of chemicals. Flounder have been found with liver lesions and fin rot, and lobsters have experienced black gill disease in Massachusetts Bays. The State of Massachusetts has issued two consumption advisories: 1) all persons should not consume the tomalley of lobsters harvested in Boston Harbor, and 2) high risk individuals should avoid all seafood harvested in Boston Harbor.

The Lower Columbia River is listed as "impaired" by the States of Oregon ad Washington due to toxic chemicals that are found in fish tissue, and the associated cancer risks. Some toxic contaminants are at levels that affect the health of certain fish and wildlife species, and may be high enough to cause human health effects.

The Sacramento River supplies 80 percent of the freshwater flow in San Francisco Bay but violates water quality criteria for copper, mercury, pesticides, and toxicity. Household pesticides have been linked to the widespread toxicity of runoff from the Bay-area cities. Automobile brake pads are likely a major source of copper in urban stormwater runoff.

Fourteen toxic substances have been identified as "pollutants of concern" in Santa Monica Bay. These include the chemicals DDT; PCBs; PAHs; chlordane; Tributyltin; chlorine; toxic metals such as cadmium, chromium, copper, lead , nickel, silver, and zinc; and hazardous substances such as oil and grease. The historical dumping of untreated industrial waste, especially DDT and PCBs, prior to implementation of the Clean Water Act has resulted in bioaccumulation in aquatic organisms, and contamination of certain seafood species. The white croaker commercial fishery is closed, there are public health warnings for recreational anglers, and there are high levels of DDT in dolphins and sea lions.

The National Estuary Programs are working to address the problem of toxic chemicals. Click here to learn more about the various management approaches the NEPs are taking towards the toxics problem.

To top of page

Habitat Loss and Degradation

Sources and Impacts

The continued health and biodiversity of marine and estuarine systems depends on the maintenance of high-quality habitat. The same areas that often attract human development also provide essential food, cover, migratory corridors, breeding/nursery areas for a broad array of coastal and marine organisms. In addition, these habitats also perform other important functions such as water quality and flood protection, and water storage. Ecosystems can be degraded through loss of habitat- such as the conversion of a seagrass bed to a dredged material island- or through a change or degradation in structure, function, or composition. Threats to habitat include conversion of open land and forest for commercial development and agriculture, forestry, highway construction, marinas, diking, dredging and filling, damming, and bulkheading. Wetland loss and degradation caused by dredging and filling have limited the amount of habitat available to support healthy populations of wildlife and marine organisms. All of these activities may cause increases in the runoff of sediments, nutrients, and chemicals. Excess nutrients such as nitrogen can lead to algal blooms that deplete oxygen and block sunlight, killing submerged aquatic vegetation.

NEP Examples
A comparison of wetland distribution in Galveston Bay between the 1950s and 1989 shows a net decrease of 19 percent (33,400 acres) of total vegetated wetlands. Subsidence, pollution, and introduction of exotic species (nutria) are suspected causes of this decline. Submerged aquatic vegetation (SAV), primarily seagrasses, decreased from 2,500 acres in the 1950s to 700 acres in 1987- a 70 percent decline.

Studies conducted through 1978 in the Barataria and Terrebonne basins in Louisiana showed that over 11,500 acres of land per year were being lost to the ocean. The rate in 1990 was estimated at almost 13,500 acres per year. Scientists have calculated that over 294,000 acres of marsh were converted to open water between 1956 and 1978. The rate of land loss currently shows a decline, however conservative estimates are that an additional 163,000 acres of land will be lost by the year 2000.

Sedimentation and invasion by introduced plant species have dramatically altered the extent and quality of saltmarsh habitat and elevated the creek bottom by over thirteen feet in Morro Bay in California. In addition, the vast majority of coastal dunes scrub has been eliminated as a result of bayside development. Recent studies on bay sedimentation have indicated that 25 percent of the bay's tidal capacity, and 66 percent of that in the delta area have been lost in the last century due to sedimentation. Sedimentation from recent fires and floods have resulted in the loss of hundreds of acres of eelgrass and oyster beds. Degradation of riparian corridors and instream habitat has occurred as a result of channelization, flood control efforts, sedimentation, and agricultural encroachment.

Evidence of damaged habitat can be found throughout Casco Bay and its watershed in Maine.

• The New Meadows "Lake", once a tidal estuary, now suffers from algal blooms due to limited tidal flushing caused by a restrictive spillway.
• Long Creek has degraded wetland areas resulting from construction of an Interstate highway.
• An Interstate crossing over the Presumpscot River has impaired the natural tidal flushing and allowed the buildup of sawdust and paper mill waste.
• Four dams on the main stem of the Royal River present barriers to fish as none have fish ladders.
• Capisic Brook used to be an American eel run but is impassable due to a dam and reduced water flows caused by sewering the areas which redirected some water flows to sewer.

The National Estuary Programs are working to address the problem of habitat loss. Click here to learn more about the various management approaches the NEPs are taking towards the habitat problem.

To top of page

Introduced Species

Sources and Impacts

Intentional or accidental introduction of invasive species may often result in unexpected ecological, economic, and social impacts to the estuarine environment. Through predation and competition, introduced species have contributed to the eradication of some native populations and drastically reduced others, fundamentally altering the food web. Overpoplation of some introduced herbiverous species has resulted in overgrazing of wetland vegetation and the resultant degradation and loss of marsh. Other impacts include: 1) alteration of water tables; 2) modification of nutrient cycles or soil fertility; 3) increased erosion; 4) interference with navigation, agricultural irrigation, sport and commercial fishing, recreational boating, and beach use; and 5) possible introduction of pathogens. Sources of introduced species include ship ballast, mariculture and aquarium trade.

NEP Examples
Four years after the first appearance of brown mussels in Corpus Christi, they had become firmly established, and their phenomenal growth has the potential to dramatically increase the maintenance requirements of navigation aids. Recently, new colonies have established in areas where salinities were thought to be prohibitive. Routine discharges from mariculture facilities may also introduce non-native species including not only the mussels, but any pathogens they may carry. In recent years, the Taura Syndrome virus has wiped out much of the shrimp farm production in Texas- the impact of exotic disease on native shrimp populations is unknown.

Australian pine, Brazilian pepper, and other introduced plant species continue to be a significant concern in Sarasota Bay due to their encroachment on native mangroves and other native wetland communities. Small, fragmented wetlands allow invasive, non-native species to become established easily. Past dredge and fill activities created spoil deposition areas that are now dominated by non-native plant species.

Waters and wetlands host well over 200 non-indigenous species in the San Francisco Estuary. These invasive species now dominate many of the estuary's ecological communities. They account for 40 to 100 percent of the species among benthic infauna and epifauna in both subtidal and intertidal areas. The Asian clam has become so abundant in San Francisco Bay that it can filter the entire water column over a significant potion of the Bay in less than a day, removing bacteria, phytoplankton, and zooplankton. Introduced cordgrasses threaten to take over much of mudflat areas, which are critical feeding sites for migratory shorebirds. The European green crab and the mitten crab, both species of concern, have been introduced to San Francisco Bay during the past ten years.

The National Estuary Programs are working to address the problem of introduced species. Click here to learn more about the various management approaches the NEPs are taking towards the invasive species problem.

To top of page

Alteration of Natural Flow Regimes

Sources and Impacts

Alteration of the natural flow regimes of tributaries can have significant effects upon the water quality and distribution of living resources in the receiving estuaries. Freshwater is an increasingly limited resource in many areas of the country. Human management of this resource has altered the timing and volume of inflow to some estuaries. Changes in the natural freshwater inflow to estuaries can have significant impacts on the health and distribution of plants and wildlife. Too much or too little freshwater can adversely affect fish spawning, shellfish survival, bird nesting, seed propagation, and other seasonal activities of fish and wildlife. In addition to changing salinity levels, inflow provides nutrients and sediments that are important for overall productivity of the estuary.

NEP Examples
The Indian River Lagoon drainage basin in Florida has doubled in size due to the construction of extensive drainage systems. Greater quantities of freshwater now enter the lagoon during storms, causing salinities to vary widely. During the wet season, salinities are often reduced over broad areas. During the dry season, flows are reduced resulting in higher salinities. These broad fluctuations in salinity can adversely affect many important estuarine species which can only survive in a narrow range of salinities. Discharges often contain large amounts of suspended materials and elevated levels of nutrients and other pollutants. Freshwater and stormwater discharges represent the largest non-point source of pollution to the lagoon. Through time, freshwater and stormwater discharges have resulted in muck deposits in the lagoon and its tributaries. These deposits are easily disturbed by wind, waves, and boat wakes, creating vast areas of turbid water and releasing trapped pollutants.

The Corpus Christi area is experiencing a "drought of record." Reservoir levels have dropped, and by agreement, the region is under "drought management conditions" which significantly curtail the freshwater releases into Corpus Christi Bay. Salinity levels have increased throughout the NEP study area. Oysters are being affected by the drought, with salinity levels higher than optimum for the eastern oyster.

Creeks entering Morro Bay in California are heavily diverted for municipal and agricultural use. Sensitive species in the creek drainages, including steelhead trout and the endangered tidewater goby, have been impacted. Water diversion from the Morro Bay watershed have increased significantly over the past thirty years. Surface diversions have resulted in massive kills of stellhead trout, and general degradation of the lower reaches of the creeks. Saltwater intrusion, though only a periodic problem, has been documented over a mile upstream from the estuary. Steelhead trout have declined significantly in the past twenty years. Water diversion, compounded by drought, is the major cause. Hydromodifications include an onstream reservoir, which significantly reduces summer surface flows, and levees which prevent streams from depositing sediment on adjacent flood plains.

In the San Francisco Bay area, tributary waters irrigate 4.5 million acres of farmland and provide drinking water to 20 million people. In recent years, more than half of the San Francisco Estuary's natural river flow has been diverted for agricultural, municipal, and industrial uses. This problem was long compounded by several years of severe drought. (However, in the last two years, California has recievied above-average rainfall.) Water diversions can severely impact environmental quality. Millions of fish eggs, larvae, and young are caught in the powerful water project pumps, and fish must contend with 1,800 unscreened diversions to farms. The timing of freshwater releases influences biological productivity, and changes in salinity can threaten drinking water quality. Insufficient flows can exacerbate the effects of pollution, and an ever-increasing population can place unrealistic demands on water supplies.

The National Estuary Programs are working to address the problem of hydrologic alteration. Click here to learn more about the various management approaches the NEPs are taking towards the freshwater inflow problem.

To top of page

Declines in Fish and Wildlife Populations

Sources and Impacts

The distribution and abundance of estuarine fish and wildlife depend on factors such as light, turbidity, nutrient availability, temperature, salinity, and habitat, and food availability. Natural and human-induced events which disturb or change environmental conditions affect the distribution and abundance of estuarine species. Declines in fish and wildlife populations have resulted from fragmentation and loss of habitats and ecosystems; pollution and decreased water quality; overexploitation of resources; and introduced species.

Habitat loss and degradation can lead to decreases in the stocks of sport and commercial fish and shellfish, changes in the populations of fur-bearing and waterfowl species, and decreased habitat for neotropical migratory birds and other species. Pollutants such as herbicides, pesticides, and other wastes pose a threat to living resources by contaminating the food chain and eliminating food sources. Runoff from farms and cities and toxic releases can alter aquatic habitat, harm animal health, reduce reproductive potential, and render many fish unsuitable for human consumption. Other threats to wildlife include oil spills, bioaccumulation of toxins, outbreaks of contagious and infectious diseases, and algal blooms such as red and brown tides. Overexploitation occurs when fisherman, trappers, hunters, or collectors take so many individuals of a species that their ability to maintain stable population levels is impaired. Introduced species compete with native species for food and habitat. Other causes of decline in fish and wildlife populations include agricultural and logging activities; trawling and bycatch; boat disturbances; entanglement from marine debris; and change in freshwater inflow.

NEP Examples
The Delaware horseshoe crab population is the largest in the world, and their eggs are a food source for the second largest stop-over population of migrating shorebirds in North America. Yet some recent population estimates indicate that the numbers of horseshoe crabs in the Delaware Bay are declining, possibly due to overharvest for use as bait. Neotropical migrant birds also utilize the Delaware Bay as a stopover area, but habitat areas have decreased by up to 40 percent due to human development. Large fisheries of anadromous species such as American shad, sturgeon, and striped bass, once existed in the Delaware Bay. However, pollution, overharvest, and damming of tributaries has led to significant declines in the populations of these species by the early part of the century. More recently, improved water quality and harvest restrictions have improved population numbers, however much still needs to be done, including additional fish passage measures in major tributaries.

Available information on commercial fishery landings shows a distinct decline in the abundance of fish and shellfish in the last 100 years in New York-New Jersey Harbor. Commercial fisheries are restricted due to toxic and pathogenic contamination. New York has closed its commercial fishery for striped bass in the Harbor, the Hudson River, and parts of the New York Bight due to concerns about PCB contamination. Commercial fishing for American eel and blue crabs is also prohibited due to toxic contamination in some areas of the Harbor. Recreational fishing is similarly restricted in the Harbor core area. Consumption advisories throughout the region provide warnings about locally-caught fish. Coastal bird and mammal populations have also seriously declined in the Harbor and the Bight. Much of the native flora and fauna of the region has been lost or drastically reduced due to the loss of coastal upland habitats.

The most acute problem facing Peconic Bay in New York is the Brown Tide which has appeared in the Flanders/Peconic and South Shore Bays, drastically reducing the scallop population. The Brown Tide has been recurring since 1985, although unpredictable in its onset, duration, and cessation, often persisting for unusually long periods of time over large areas. By 1988, the Brown Tide had decimated the nationally significant harvest of scallops, with virtually no landings reported. Clams are also adversely impacted, although to a lesser degree than scallops. Brown Tide may also adversely affect other species such as finfish due to reduced visibility.

In Tillamook Bay, Oregon, chum, coho, and steelhead trout stocks are listed as depressed in the basin. Historically, the Tillamook Basin was an important producer of coho salmon, with runs averaging more than 150,000 fish. Fewer than 300 adult spawners were observed annually from 1990 to 1992. Gill net fishery landings averaged over 45,000 coho annually in the 1920s and 1930s. By the 1980s and early 1990s, landings were estimated at only 19,000 fish per year. Past studies have identified the following factors which may reduce or degrade fish habitat: 1) poorly placed dikes; 2) forest fires; 3) logging and road construction; 4) loss of slough habitat; 5) increased sedimentation from watershed erosion; 6) the Bayocean Spit breach; and 7) subsequent changes in bay circulation and salinity. Possibly the most important factor to affect past and present conditions in the watershed was a series of forest fires earlier this century which affected 63 percent of the basin and reduced habitat, protective cover, and nutrient input. Other factors which may have affected coho populations include the high historic harvest rate and the effects of hatchery releases.

The National Estuary Programs are working to address the problem of fish and wildlife declines. Click here to learn more about the various management approaches the NEPs are taking towards the wildlife problem.

To top of page