The Ecological Condition of

Estuaries in the

Gulf of Mexico

United States

Environmental Protection

Agency

Office of Research and

Development

Washington DC 20460

EPA

EPA 620-R-98-004

July 1999

www.epa.gov

© Don Baccus
EPA 620-R-98-004

July 1999

The Ecological Condition of Estuaries in

the Gulf of Mexico

U.S. Environmental Protection Agency

Office of Research and Development

National Health and Environmental Effects Research Laboratory

Gulf Ecology Division

Gulf Breeze, Florida 32561

Interagency Agreement #DW14938557

J. Kevin Summers, Project Officer

This study was conducted in cooperation with

Department of Interior, United States Geological Survey,

Biological Resources Division

Gulf Breeze Project Office

National Health and Environmental Effects Research Laboratory

 Office of Research and Development

 U.S. Environmental Protection Agency

Washington, D.C. 20460
ii

Disclaimer

The U.S. Environmental Protection Agency through its Office of Research and Development,

funded and collaborated in the research described here under Interagency Agreement

DW14938557 with the Department of Interior, U.S. Geological Survey, National Wetlands

Research Center. It has been subjected to the Agency’s peer and administrative review and

has been approved for publication as an EPA document.

Mention of trade names or commercial products does not constitute endorsement or

recommendation for use.

This report should be cited as:

USEPA. 1999. Ecological Condition of Estuaries in the Gulf of Mexico. EPA 620-R-98-

004. U.S. Environmental Protection Agency, Office of Research and Development, National

Health and Environmental Effects Research Laboratory, Gulf Ecology Division, Gulf Breeze,

Florida. 
iii

Acknowledgments

This report, The Ecological Condition of Estuaries in the Gulf of Mexico, was prepared

collaboratively by staff from the U.S. Environmental Protection Agency (USEPA) and the

U.S. Geological Survey (USGS). The staff included Virginia Engle, John Macauley, and

Kevin Summers from the Gulf Ecology Division (GED), National Health and Environmental

Effects Research Laboratory, Office of Research and Development, USEPA, Gulf Breeze,

Florida and Pete Bourgeois, through an Interagency Agreement with the Gulf Breeze Project

Office, National Wetlands Research Center, Biological Resources Division, USGS, Gulf

Breeze, Florida. The report was coordinated through the Gulf of Mexico Program, Stennis

Space Center, Mississippi, and its partners, including USEPA Regions 4 and 6, and USEPA

Office of Water, Florida Department of Environmental Protection, Alabama Department of

Environmental Management, Mississippi Department of Environmental Quality, Louisiana

Department of Environmental Quality, Texas Natural Resources Conservation Commission,

Texas Parks and Wildlife, and Texas Water Development Board. Data was obtained from

these and other sources, including the National Oceanic and Atmospheric Administration,

U.S. Fish and Wildlife Service, Minerals Management Service, and U.S. Bureau of the

Census. All data sources are listed at the end of this report.

We would like to thank the following people for their invaluable assistance in putting this

report together: Lois Haseltine, Reneé Conner, and Linda Harwell, Johnson Controls World

Services for desktop publishing, graphics support, and database management; Steve Robb,

USGS for geographic information systems support; Shannon Price, Johnson Controls World

Services, Beth Vairin, USGS, Sheila Howard, National Caucus and Center on Black Aged,

Inc., and James Harvey, USEPA, for technical editor support. Special thanks go to the

technical reviewers of this report: Foster Mayer, Raymond Wilhour, Larry Goodman, and

William Walker of USEPA/GED; James Giattina, Gulf of Mexico Program; John Carlton,

Alabama Department of Environmental Management; Kenneth Haddad, Florida Department

of Environmental Protection; Phil Bass, Mississippi Department of Environmental Quality;

Greg Steyer, Louisiana Department of Environmental Quality; Holly Greening, Tampa Bay

National Estuary Program; Nancy Rabalais, Louisiana Universities Marine Consortium;

Kerry St. Pé, Barataria-Terrebonne National Estuary Program; Larry McKinney, Texas Parks

and Wildlife Department; and Terry Wade, Texas A&M University Geochemical and

Environmental Research Group.

Cover photo of shrimp boat, aerial marsh landscape, and blue crab USGS/NWRC

Cover photo of Snowy Egret ©Don Baccus (dhogaza@pacifier.com) donb.photo.net/photo_cd/d/b4.html
iv

Acronyms

USEPA U.S. Environmental Protection Agency

EMAP Environmental Monitoring and Assessment Program

EMAP-E Environmental Monitoring and Assessment Program - Estuaries

NEP National Estuary Program

NERRS National Estuarine Research Reserve System

NPDES National Pollution Discharge Elimination System

NOAA National Oceanic and Atmospheric Administration

ADEM Alabama Department of Environmental Management

ALAMAP Alabama Monitoring and Assessment Program

R-EMAP-TX Regional Environmental Monitoring and Assessment Program - Texas

NSSP National Shellfish Sanitation Program

MNET Gulf of Mexico Aquatic Mortality Network

USGS United States Geological Survey

CCMP Comprehensive Conservation and Management Plan

OCS Outer Continental Shelf

AVHRR Advanced Very High Resolution Radiometer

DO Dissolved Oxygen

HAB Harmful Algal Bloom

NSP Neurotoxic Shellfish Poisoning

ER-L Effects Range - Low (Long et al. 1995)

ER-M Effects Range - Median (Long et al. 1995)

PAH Polycyclic Aromatic Hydrocarbon

PCB Polychlorinated Biphenyl

DDT Dichlorodiphenyltrichloroethane

TBT Tributyltin

SAV Submerged Aquatic Vegetation
v

Executive

Summary

The Gulf of Mexico is a vast natural resource encompassing the coastal areas of western Florida,

Alabama, Mississippi, Louisiana, and Texas, as well as a portion of Mexico. Many estuaries flow

into the Gulf of Mexico and serve as nursery grounds for fish, habitat for a wide variety of wildlife,

shipping routes, and a source of recreation. Estuarine-dependent species constitute more than 95

percent of the commercial fishery harvests from the Gulf of Mexico, and many important recreational

fishery species depend on estuaries during some part of their life cycle. Gulf estuaries are diverse

and productive ecosystems that provide a variety of valuable resources, including fish and shellfish,

recreation, transportation, and water supply.

Assessing the overall condition of Gulf of Mexico estuaries required incorporating data from other

federal, state, and local monitoring programs to augment the information on ecological indicators

collected by the U.S. Environmental Protection Agency’s (USEPA) Environmental Monitoring and

Assessment Program (EMAP). The resulting document would provide a synthesis of the available

knowledge about the condition of Gulf of Mexico estuaries. This document is intended for use by

scientists and other citizens concerned with the ecological condition of estuaries, as well as by

managers and lawmakers interested in the sustained use of estuaries for commercial and recreational

purposes. It also addresses public concerns about the aesthetic quality of coastal areas vital to

tourism and recreation. By producing this report on the ecological condition of estuaries in the Gulf

of Mexico, we have taken one step in assessing the health of this environmental resource. We have

produced an environmental “report card” to be used as a guide in the evaluation of management

decisions and research directions. 

This report is organized in three parts: (1) an introduction that gives background information on the

Gulf of Mexico, estuarine ecology, and the factors that impact estuaries in the gulf, (2) the main

section on priority ecological indicators used to measure the condition of estuaries in the gulf and (3)

an ecological report card that summarizes the data on ecological indicators and provides a rating of

the condition of estuaries in each gulf state and for gulf estuaries overall. Many of the ratings were

based on the percent area of estuaries in each state exhibiting degraded or adverse levels of an

indicator.

Eutrophication, a condition of high nutrients often resulting in low oxygen levels and other adverse

effects, is an important water quality concern for estuaries along the gulf coast. The National

Oceanic and Atmospheric Administration (NOAA) has compared the Gulf of Mexico to other coastal

regions like the middle Atlantic and has ranked the Gulf of Mexico as having the highest number of

point sources of nutrients and the highest percentage of land use devoted to agriculture. We

evaluated monitoring data for nitrogen, chlorophyll, and dissolved oxygen as indicators of

eutrophication. Although most of the estuaries exhibited high nitrogen or chlorophyll or low
Executive Summary

vi

dissolved oxygen concentrations at least once during a survey, many times these conditions were

observed in small rivers or bayous rather than in the entire estuary. Often, the percent area affected

was low. The gulf estuaries had moderate conditions overall for nutrients and dissolved oxygen. 

Definite nutrient problems were observed in >25% of the estuarine area in Louisiana and Texas and

definite dissolved oxygen problems were observed in Alabama.

Contaminants in estuarine sediments provide evidence of the accumulation of chemicals from

anthropogenic sources. We compared the concentrations of sediment contaminants to established

guideline values to determine the proportion of estuarine area that could have potential adverse

effects on living organisms. Although detectable levels of contaminants were measured in almost

every estuary in the Gulf of Mexico, <25% of the estuarine area in all states had contaminant

concentrations that exceeded these guidelines. 

Wetlands are integral parts of estuarine systems. Declining acreage means habitat loss that may be

the result of commercial and residential development, hydrologic alterations, or dredge and fill

operations. The Gulf of Mexico region contains more than 50% of the coastal wetland acreage in the

U.S. and yet it also has the highest rate of coastal wetland loss. Nine of the top ten estuarine drainage

areas ranked by total wetland area are in the Gulf of Mexico region. The most current estimates of

total wetland loss over the past 200 years range from 41% to 54% for the gulf states. Although

coastal wetlands continue to be altered or destroyed, some estimates indicate that the rate of loss has

slowed. All gulf states were rated as having severe problems with wetland loss.

The condition of benthic (bottom-dwelling) invertebrates, fish and shellfish, birds, and threatened

and endangered species was used to evaluate the health of estuarine fauna. Degraded benthic

communities inhabited <25% of the estuarine area in all gulf states except for Texas. Commercial

fish and shellfish landings may be used as an indicator of population stability while fish biomarkers

are used to measure the health of individuals in the population. Commercial landings of the top four

fisheries (shrimp, menhaden, blue crab, and oyster) are stable in the gulf states while fish biomarkers

indicate fair to poor fish health in Alabama and Texas and good fish health elsewhere. Coastal and

marine bird populations appear to be in good condition throughout the gulf. Four threatened or

endangered species inhabit coastal areas in the Gulf of Mexico: brown pelican, Gulf sturgeon,

manatee, and Kemp’s ridley sea turtle. In general, populations of these species are in good to fair

condition in the gulf states.

Public health indicators include shellfish bed closures and chemicals found in edible fish tissue. 

Harvest of shellfish (primarily oyster in the Gulf of Mexico) is restricted or prohibited when

concentrations of bacteria or other pathogens reach levels that could impair human health. The gulf

states contain the most acreage of shellfish-growing waters in the U.S. but also have the most acreage

restricted for harvest. All gulf states except Mississippi have >25% of their shellfish-growing waters

restricted for harvest, mostly due to pollution from wastewater treatment plants or other upstream

sources. Advisories may be issued that limit consumption when the concentrations of chemicals in

fish tissue exceed levels known to be harmful to humans. Although seafood consumption advisories

have been issued in all gulf states, the percent of the fish population with high concentrations of

contaminants is relatively low in the gulf overall.
vii

Table of Contents

Disclaimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Acronyms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv

Executive Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Introduction .......................................... 1

Estuaries and Their Value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Population Distribution ................................... 5

Consequences of Human Usage ............................ 6

Land Use Patterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Natural Habitat Characteristics ............................. 9

Federal Response to Concerns about Estuaries . . . . . . . . . . . . . . . . 11

Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Freshwater Inflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Water Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Eutrophication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Chlorophyll a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Harmful Algal Blooms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Sediment Contaminants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Habitat Change . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Wetlands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Submerged Aquatic Vegetation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
viii

Biological Integrity .................................. . 33

Benthos .............................................. . 33

Commercial and Recreational Fisheries ..................... . 35

The Red Drum Fishery .................................. . 36

Fish Biomarkers ....................................... . 37

Coastal and Marine Birds ................................ . 38

Threatened and Endangered Species ....................... . 40

Public Health ....................................... . 43

Shellfish - Growing Waters ............................... . 43

Contaminants in Fish and Shellfish ........................ . 44

Fish Kills ............................................. . 46

Ecological Report Card ............................... . 47

Data Sources ....................................... . 53

Appendix I: National Estuary Programs .................... . 65

Appendix II: Characteristics of Estuaries in the Gulf of Mexico . . 69
Introduction

1

Introduction

The U.S. Gulf of Mexico region encompasses two biogeographical provinces: 1) The

Louisianian Province which covers estuarine systems from Rio Grande, Texas, to Anclote

Key, Florida and 2) the West Indian province which includes the western Florida coast from

Tampa Bay to the Florida Keys (Fig. 1; estuaries in Mexico were not included in this

assessment). This expanse includes many large estuarine systems (surface area > 280 km2)

such as Corpus Christi Bay, Galveston Bay, Sabine Lake, Vermilion-Atchafalaya Bay,

Terrebonne Bay, Barataria Bay, Breton Sound, Lake Pontchartrain, Mobile Bay, Pensacola

Bay, Choctawhatchee Bay, Tampa Bay, and Florida Bay, in addition to several hundred small

estuaries.

Estuaries are bodies of water that are balanced by freshwater and sediment influx from rivers

and the tidal actions of the oceans, thus providing transition zones between the freshwater of

a river and the saline environment of the sea. The result of this interaction is an environment

where estuaries, along with their adjacent marshes and seagrasses, provide a highly

productive ecosystem, that supports wildlife and fisheries and contributes substantially to the

economy of coastal areas. As spawning, nursery, and feeding grounds, estuaries are

invaluable to fish and shellfish. Estuarine-dependent species constitute more than 95 percent

of the commercial fishery harvests from the Gulf of Mexico, and many important recreational

fishery species depend on estuaries during some part of their life cycle. Gulf estuaries are

diverse and productive ecosystems that provide a variety of valuable resources, including fish

and shellfish, recreation, transportation, and petroleum and minerals.

What began as an overall summary of the activities of the USEPA’s Environmental

Monitoring and Assessment Program for Estuaries (EMAP-E) in the estuaries of the

Louisianian and West Indian provinces (the Gulf of Mexico and south Florida) has evolved

into the report you see here. One of EMAP-E's goals was to assess ecological conditions

using environmental monitoring data from multiple spatial and temporal scales. From 1991

to 1995 EMAP collected data on ecological indicators from estuaries in the Gulf of Mexico. 

The ecological condition of these estuaries was reported in annual statistical summaries that

enumerated areas found to have deleterious conditions (e.g., low dissolved oxygen, degraded

benthic habitat, or contaminated sediments). 

Evidence of the diminishing quality of our estuaries has been found in the large amounts of

debris washing up on shores; beach closures due to trash, bacteria, or red tide; reduced water

clarity and water quality; fish consumption advisories issued to warn consumers of

contaminated fish; shellfish bed closures; and fishing bans. This evidence contributes to the

public’s perception that something must be done to restore our estuaries to a healthy state. In 
2

Fig. 1. Estuarine systems located in the Gulf of Mexico (United States; NOAA 1997).
Introduction

3

order to effectively gauge whether future management actions are improving the situation,

however, a baseline for gulf-wide estuarine conditions must first be established. The current

report focuses on the ecological condition or health of estuaries in the Gulf of Mexico, using

indicators that are well established in the scientific community and incorporating both the

most current information and historical trend data where available. This report provides

much-needed information to scientists and others concerned with the ecology of estuaries,

and to managers and lawmakers concerned with the sustained use of estuaries for commercial

and recreational purposes. It will also address public concerns about the aesthetic quality of

coastal areas that are vital to tourism and recreation. 

Estuaries and Their Value

Estuaries and wetland environments are intertwined. Coastal emergent wetlands border

estuaries and the Gulf of Mexico and include tidal saltwater and freshwater marshes and

mangroves. Encompassing over two million hectares (five million acres or more than half of

the national total), the Gulf of Mexico coastal wetlands serve as essential habitat for a diverse

range of species. These wetlands are used by shorebirds, migratory waterfowl, fish,

invertebrates, reptiles, and mammals. A large percentage of the migrating waterfowl and

migrant Neotropical birds of the U.S. utilize these coastal habitats. Mudflats, salt marshes,

mangrove swamps, and barrier island habitats also provide year-round nesting and feeding

grounds for abundant populations of gulls, terns, and other shorebirds. Gulf estuaries and

marshes and associated watersheds provide habitat for many threatened and endangered

species, including sea turtles (e.g., leatherback, hawksbill, Kemp’s ridley, loggerhead, and

green), piping plover, bald eagle, brown pelican, Gulf sturgeon, West Indian manatee, and

American crocodile. Estuaries and wetlands support complex food webs that provide an

abundant food source for juvenile and adult fishes (Fig. 2). In addition to providing habitat,

wetlands also improve water quality by filtering pollutants and sediment and offer a buffer

zone to protect upland areas from flooding and erosion. 

Estuaries provide humans with a variety of uses. They both supply water and provide a point

of discharge for municipalities and industries, and support agriculture, commercial and sport

fisheries, and recreational uses such as swimming, diving, and boating. The complex

network of channels and wetlands within the gulf shoreline provides habitat for estuarinedependent commercial and recreational fisheries. In the Gulf of Mexico commercial and

recreational fisheries and tourism are economically important. Tourism in the gulf coast

states contributes an estimated $20 billion to the economy each year. The Gulf of Mexico

ranks second only to Alaska in total commercial landings. The rich waters yielded

approximately 684 million kg (1.51 billion pounds) of fish and shellfish in 1996. This

represented at least a two-fold increase in the commercial landings of fish in the gulf since

1950, with the peak years from 1982 to 1987 yielding more than one billion kg of fish and

shellfish annually (Fig. 3). Worth more than $689 million at dockside, the 1996 harvest

represented 33% of the total annual domestic harvest (excluding Alaska) of commercial fish. 
Introduction

4

Fig. 2. Conceptual diagram of the food web in Gulf of Mexico estuaries (redrawn from Weber, et al.,

1992).

Fig. 3. Commercial landings in million kg of all species

from Gulf of Mexico waters from 1950 to 1996 (National

Marine Fisheries Service).

The gulf boasts the largest and most valuable shrimp fishery in the U.S. (99 million kg or

69% of the national total in 1996) and also contributed 57% of total oyster production in the

U.S. in 1996. Other important gulf

fisheries include crabs and spiny

lobsters, menhaden, herring, mackerel,

tuna, grouper, snapper, drum, and

flounder. The entire Gulf of Mexico

fishery yields more finfish, shrimp, and

shellfish annually than the south and

mid-Atlantic, Chesapeake, and Great

Lakes regions combined. The gulf’s

waters draw millions of sport fisherman

and beach users each year. It is

estimated that the gulf supports more

than one-third of the national marine

recreational fishing, hosting 4.8 million

anglers in 1995, who caught an

estimated 42 million fish. 
Introduction

5

Fig. 4. Population estimates based on the 10-

year Census for coastal counties in the Gulf of

Mexico (U.S. Census Bureau).

Gulf oil and gas production are equally valuable to the region’s economy and are a critical

part of the nation’s total energy supply. In 1990, more than 1,600 Outer Continental Shelf

(OCS) leases were in production (Melancon et al 1997). OCS royalties from the Gulf of

Mexico annually contribute about $3 billion to the Federal Treasury. The Gulf of Mexico

ranks second only to Alaska in terms of potential petroleum reserves, contributing 13% of the

U.S. domestic oil and gas production in 1994 (Lore et al 1996). The Minerals Management

Service projects a doubling in Gulf of Mexico oil production by the year 2000. Petroleum

and chemical products also constitute the majority (69%) of shipping tonnage that passes

through gulf ports and harbors. 

Shipping and marine transport is an important industry in the gulf. Seven of the top ten

busiest ports in the U.S. in terms of total tonnage are located in gulf estuaries (Port of South

Louisiana, Houston, Baton Rouge, New Orleans, Port of Plaquemines, Corpus Christi, and

Tampa). Shipping tonnage in the gulf has increased from 83 million tons in 1982 to 118

million tons in 1995 with 98% of the traffic traveling via the intracoastal waterway.

Population Distribution

Millions of people live along the Gulf of

Mexico coastline, attracted by its shorelines

and waterways, temperate climate, and

abundant resources. The 1990 census

indicated that coastal counties in the Gulf of

Mexico accounted for only 11% of the

nation’s total coastal population and had the

lowest population density (187 persons per

square mile) of all coastal regions of the

continental U.S. (i.e., northeast, southeast,

Great Lakes, and Pacific, excluding Alaska

and Hawaii). The coastal counties in the gulf

are experiencing the second fastest rate of

growth; between 1970 and 1980, the

population grew by more than 30 percent, and between 1980 and 1990, the population grew

by more than 16% (Fig. 4). Texas and Florida have the largest populations in coastal

counties of the Gulf of Mexico and similar relative growth rates (Fig. 4). All but four coastal

counties in Florida had more than a 100% increase in population from 1950 to 1990 (Fig. 5). 

According to projections by the U.S. Department of Commerce, the gulf’s total coastal

population will increase by 144 percent between 1960 and 2010, to almost 18 million people. 

This increase in population is a concern due to the added impacts and competing needs for

the gulf’s natural resources.

A growing population will require land to expand into, converting other habitats such as

forest or agriculture to urban areas. Increased housing and road construction puts pressure on

the receiving waters that have to assimilate the additional storm water runoff from the
Introduction

6

Fig. 5. Percent change in population from 1950 to 1990 in counties of Florida, Alabama, Mississippi,

Louisiana, and Texas (U.S. Census Bureau).

expanding impervious surfaces associated with urbanization. A growing population also

generates more wastewater and solid waste that require disposal and increase emission of

pollutants to the air. Pollutants carried in water runoff and by atmospheric deposition affect

the health of estuaries. 

Consequences of Human Usage

The ability of estuaries to function as nursery grounds depends upon the quantity, timing, and

location of freshwater inflows. Estuarine ecosystems are impacted by humans, primarily via

upstream withdrawals of water for agricultural, industrial, and domestic purposes;

contamination by industrial and sewage discharges and agricultural runoff carrying pesticides

and herbicides; eutrophication caused by excessive nutrient inputs from a variety of nonpoint

(agricultural drainage, faulty septic systems) and point sources (sewage treatment plants); and

habitat alterations (e.g., construction and dredge and fill operations). Common effects of

human use of estuaries include degraded natural habitats, declining plant and animal

populations, diminishing fish and shellfish harvests, and impaired water quality. These
Introduction

7

effects are clearly observable in some estuaries of the Gulf of Mexico. Growth of human

populations in the estuarine watersheds, combined with industrial and agricultural discharges,

places more demands on the natural resources. In some areas, estuaries are unable to safely

assimilate the amounts of pollution being added to the system and become adversely affected. 

Most problems observed in estuaries are related to land use practices and to human

population density.

Land Use Patterns

Understanding land use within watersheds is a prerequisite to understanding the ecological

condition of Gulf of Mexico estuaries. Gulf estuaries encompass approximately 30,000 km2

(42% of the total estuarine surface area of the U.S. excluding Alaska). Including the

Mississippi River, the Gulf of Mexico drainage area encompasses more than 4 million km2 or

more than 55% of the total area of the conterminous U.S. (Fig. 6). The Gulf of Mexico

receives an average of 27,473 cubic meters per second of freshwater inflow daily (more than

50% of the daily average for the continental U.S.). Although the land use within the entire

watershed determines what materials are carried by runoff into estuaries, we estimated the

percent area that was classified into land use categories of just the five gulf states and not the

entire watershed. Forest and agriculture comprise approximately 58% of the land area in the

five gulf states (Fig. 7). While forests provide filtration for sediment and nutrients from

runoff, as well as structure to stabilize shoreline and reduce erosion, many of the forests are

in areas distant from the shores of the estuarine waters. Many are being replaced by urban and

agricultural expansion.

Effects of human use on estuaries:

 Texas, Louisiana, and Alabama ranked first, second, and fourth in the nation in 1995 in

terms of discharging the greatest amounts of toxic chemicals.

 More than half of the oyster producing areas along the gulf coast are permanently or

conditionally closed. These closure areas are growing as a result of increasing human and

domestic animal populations along the gulf coast.

 Diversions and consumptive water use for human activities have resulted in significant

changes in the quantity and timing of freshwater inflows to the Gulf of Mexico habitats.

 Louisiana is losing valuable coastal wetlands at the rate of approximately 65 km2

 (25 mi2)

per year.

 Up to 18,000 km2

 (7,000 mi2) of oxygen deficient (hypoxic) bottom waters have been

documented off the Louisiana and upper Texas coasts.

Source: Gulf of Mexico Program, 1994.
Introduction

8

Fig. 7. Satellite Advanced Very-High Resolution Radiometer (AVHRR) image of vegetation types in the gulf

coast states (USGS Earth Resources Observation Systems Data Center).

Fig. 6. Sources of freshwater inflow into the Gulf of Mexico from the Mississippi River and 

non-Mississippi watersheds. (USEPA, Region 6)
Introduction

9

Agricultural land can be divided into pasture and cropland. Pasture land consists of grassy

areas for raising and feeding livestock, while cropland consists of cultivated areas which

provide various food products. Other land uses include wetland habitats (17%) and urban

areas (5%) that are generally located close to the coastline.

Natural Habitat Characteristics

Salinity, temperature, water depth, and sediment type are the primary natural habitat

characteristics that affect estuaries. Water depth affects the distribution of shellfish and

submerged aquatic vegetation. Salinity is influenced by rainfall and tidal surges and affects

the distribution of benthic animals, fish, and plants. Temperature is relatively stable in Gulf

of Mexico estuaries, but changes in temperature can influence when animals feed, reproduce,

move locally, or migrate. Sediment type is an important factor determining the composition

of the benthic community and in the sediment’s potential for absorption and adsorption of

contaminants.

 Average water depth of estuaries in the Gulf of Mexico is 3 m, with maximum depths

(greater than 10 m) occurring in dredged shipping channels and the Mississippi River.

 Gulf sediments change from terrigenous to carbonate as one goes from west to east. 

EMAP’s survey of estuarine sediments found that they are primarily mud (more than 80%

silt-clay) and mixed mud-sand (20-80% silt-clay) from Tampa Bay, Florida, to the Rio

Grande, Texas (Fig. 8). In south Florida, however, sediments are primarily sand (less

than 20% silt-clay).

 Water clarity is valued by society and contributes to the maintenance of productive

biological communities. We define low water clarity as less than 10% transmission of

ambient light at 1m depth or water in which divers would not be able to see their hands

when held at arm’s length. Moderate water clarity is defined as 10-25% transmission of

ambient light at 1m depth or as water in which waders are unable to see their feet in

waist-deep water. Few gulf estuaries have low water clarity (Fig. 8).

 Estuaries are characterized by gradients in salinity from near fresh water at the mouths of

tributaries to near marine at the mouth of the estuary. Gulf of Mexico estuaries are

predominantly polyhaline (more than 18 ppt) during the summer months (Fig. 8).

 Shallow estuaries are less able than are deeper ones to store heat, and water temperature

fluctuates from 4 to 32°C annually. 

 Stratification of the water column occurs when layers of water with different salinity or

temperature do not mix. In the gulf this usually occurs during the summer but is highly

variable and often diurnal in nature. Benthic organisms are exposed to rapidly fluctuating

dissolved oxygen and salinity due to tides and inflow.
Introduction

10

Fig. 8. Distribution of sediment characteristics, water clarity, and salinity condition in

estuaries from the Gulf of Mexico. Percentages represent percent area of the Louisianian

Province (Tampa-Rio Grande) and the West Indian Province (South Florida); USEPA

EMAP-E Database for the Louisianian [1991-1994] and West Indian [1995] Province.
Introduction

11

Federal Response to Concerns about Estuaries

In 1987, the National Estuary Program (NEP) was started by the USEPA “to protect and

restore the health of estuaries while supporting economic and recreational activities.” Since

then, seven NEP’s (Fig. 9) have been established in the Gulf of Mexico, representing

partnerships between government agencies responsible for managing estuarine resources and

people who depend on estuaries for their livelihood and quality of life. EMAP focused much

of its early efforts on determining the status of estuarine habitats nationwide. More recently,

attention has been focused on estuaries by the Estuary Habitat Restoration Partnership Act

(S.1222, introduced in Congress in 1997), which is specifically designated to provide

assistance to communities to restore estuarine habitat. 

To achieve the goals of the NEP, the USEPA helps create local

partnerships between government agencies responsible for managing

estuarine resources and the people who depend on the estuaries for

their livelihood and quality of life. A major benefit of the NEP is

that it brings communities together to decide the future of their own

estuaries. Citizens, business leaders, educators, and researchers

work with representatives from government agencies to identify

their estuary’s problems and to recommend solutions. Each NEP

formulates a Comprehensive Conservation and Management Plan

(CCMP) that serves as a blueprint for revitalizing the estuary and

protecting it from new dangers. The Gulf of Mexico NEP’s are demonstrating practical and

innovative ways to revitalize and protect their estuaries (see Appendix 1 for brief descriptions

of individual NEPs).

Recognizing the natural value of estuaries, Congress created

the National Estuarine Research Reserve System (NERRS)

in 1972. NERRS is dedicated to fostering a system of

estuary reserves that represents the wide range of coastal and

estuarine habitats found in the U.S. and its territories. In

pursuit of this goal, NERRS works with federal and state

authorities to establish, manage, and maintain reserves, and

to provide for their long-term stewardship. Research and

education are also crucial to meeting this goal. Reserves in

the system serve as laboratories and classrooms where the

effects of both natural and human activity can be monitored

and studied. To date, 22 estuaries nationwide have been

designated as NERRS, 3 of which are located along the gulf

coast (Fig. 2; see Appendix 1 for brief descriptions of

individual NERRS).
Introduction

12

Fig. 9. Locations of National Estuary Programs and National Estuarine Research Reserve Systems in the

Gulf of Mexico (USEPA).

Summary

This overview of the estuarine resource characteristics in the Gulf of Mexico sets the context

within which to describe the state of the Gulf of Mexico estuaries. For example, a

combination of environmental factors may underlie changes in fish abundance, size, and

species composition in estuaries. Among these factors are turbidity (water clarity) from

resuspension of sediments and phytoplankton growth, salinity, depth, temperature, nutrient

enrichment, and pollution. Susceptibility of fish to poor water quality is, in part, determined

by the estuarine characteristics. This report provides a review of the state of the estuarine

environment in the Gulf of Mexico region. This is a summary of historical information and

of our current state of knowledge about a set of indicators of estuarine condition for water

and sediment quality, habitat change, condition of living resources, and aesthetic quality. 

Each indicator is briefly discussed relative to its importance for understanding estuarine

condition; then the current condition of the indicator is summarized. Each indicator is then

used to assess the status of estuarine condition relative to the indicator. This report is an

assessment of the health of estuaries in the Gulf of Mexico based on historical and current

conditions. It serves to emphasize how important estuaries are and why we should continue

to preserve, protect, and correct problems within the gulf’s estuaries.
13

Freshwater

Inflow

Estuaries function as transition zones

between the freshwater of a river and the

saline environment of the sea and, by

definition, receive freshwater inflows. 

The ability of an estuary to function

properly and to sustain populations of

animals and plants depends on the

quantity, quality, timing, and location of

freshwater inflows. The effects of the

diversion of freshwater inflow is of great

concern to resource managers. Whether

freshwater inflow is diverted away from

an estuary (e.g., for agriculture or water

supply) or into an estuary (e.g., effluent,

river discharge diversion), the effects

upon an estuary include habitat loss,

changes in salinity, and altered nutrient

and sediment loads. These changes

affect wetlands, phytoplankton, zooplankton, benthos, and fish directly and indirectly by altering

suspended sediments, dissolved oxygen, water temperature, pH, and water clarity.

The areas throughout the Gulf of Mexico that have been most adversely affected by alterations in

freshwater inflow are Florida Bay, the Louisiana coastal marshes, and the Texas gulf coast. Florida

Bay receives freshwater inflow from the Everglades, where the natural sheet flow through this

wetland has been altered by canals and water management structures. Seagrass die-off, a declining

shrimp fishery, algal blooms, and fish kills in Florida Bay have been attributed to the effects of

altered freshwater inflow. The vast majority of the freshwater inflow to the Gulf of Mexico comes

through the Mississippi River delta. Historically, the natural flow from the Mississippi River

deposited sediments on the coastal marshes and deltas of Louisiana; this accretion of sediment

countered the loss of land due to subsidence. The Mississippi River’s flow is now controlled and

managed by levees and dikes. Because of this change in the natural flow, sediments from the

Mississippi River are now deposited in the Gulf of Mexico, and the rate of land loss exceeds the rate

of accretion in Louisiana’s coastal wetlands. In Texas, reduced freshwater inflow to estuaries is of

concern to resource managers primarily because of the adverse effects of salinity changes on

commercial fish and shellfish as well as other estuarine species. Altered freshwater inflow indirectly

affects the metabolism, reproduction, and migration of fish and shellfish as well as other organisms

that inhabit estuaries. Texas state agencies are currently assessing the freshwater inflow

requirements of estuaries in order to sustain a healthy ecosystem and productivity of fish, shellfish,

and other estuarine life.

Functions of freshwater inflow in estuaries:

 Provide a food supply by stimulating both

photosynthesis and microbial

decomposition;

 Deposit sediments that stabilize coastal

wetlands against erosion, subsidence, and

sea level rise;

 Drive estuarine circulation and establish

salinity gradients; and

 Create a range of salinities under which

plants and animals thrive.

Source: Gulf of Mexico Program, 1994.
14
15

Fig. 10. Summary of classification of estuaries in

terms of water quality from 1996 305(b) reports

submitted by Florida, Alabama, Mississippi,

Louisiana, and Texas.

Water Quality

In the 25 years since the passage of the

Clean Water Act, billions of pounds of

pollution have been prevented from

entering waterways and the number of

rivers lakes, streams, and estuaries that

are safe for swimming and fishing has

doubled (USEPA 1997). Pursuant to

Section 305(b) of the Clean Water Act,

the states must report on the status of

water quality in their jurisdiction every 2

years. The results from the 1996

assessment of water quality in estuaries

and coastal waters of the Gulf of Mexico

are shown in Fig. 10. Estuaries are

classified according to their designated

beneficial uses, which represent the

desirable activities that water quality

should support. For estuaries these

include primarily aquatic life support, fish

consumption, or recreation. States may

require an individual estuary to support

multiple uses. The states are responsible

for conducting monitoring and assessment

programs to evaluate whether or not the

water quality in estuaries is fully,

partially, or not supporting of the

designated uses. In addition, the states

identify indicators that document the

impact of water quality degradation.

States also identify pollutants or processes

that are responsible for degraded water

quality. The percent of a state’s estuaries

that has impaired water quality when

tracked over time is a good indicator of

whether or not efforts to improve

estuarine water quality are successful. Of

the 78% of total estuarine area in the gulf
Water Quality

16

Fig. 11. Conceptual diagram of the conditions that may

lead to eutrophication in estuaries (redrawn from USEPA,

1998; D.O. = Dissolved Oxygen).

that was surveyed in 1994-95, 65% fully supported designated uses. Of the estuarine area

that was impaired (35%), most of the impairment came from pathogen indicators (e.g. fecal

coliform) and eutrophication indicators (e.g. nutrients, organic enrichment, and low dissolved

oxygen). The primary sources of impairment of estuaries included municipal and industrial

point sources as well as nonpoint sources like urban runoff, agriculture, and land disposal

from septic tanks.

Evaluating the water quality in estuaries involves many levels of monitoring and regulation

including National Pollution Discharge Elimination System (NPDES) permits for discharges

into estuaries; evaluation of wastewater treatment plant effluent; and monitoring for bacteria

(fecal coliform), salinity, and dissolved oxygen. The water quality of estuaries affects all

classes of biota that inhabit this ecosystem, including humans. The quality of estuarine

waters determines whether or not (1) we can consume the fish and shellfish from estuaries,

(2) we can swim safely without fear

of infection, (3) we can inhabit

waterfront property without the

aesthetic nuisance of algal blooms,

noxious odors, or masses of dead and

decaying fish, and (4) all levels of

biota in the estuarine food web can

exist in a healthy, stable environment. 

Some of these water quality issues

will be discussed in a later section on

public health.

Eutrophication

Some nutrient inputs to coastal waters

are necessary for a healthy, functional

estuarine ecosystem. When

sediments, sewage, or fertilizers are

introduced into an estuary, however,

the concentration of available

nutrients can increase beyond natural

background levels, resulting in a

condition known as eutrophication

(Fig. 11). Even relatively modest

increases in the concentration of

nitrogen or phosphorus may be

sufficient to trigger an algal bloom. 

In addition to being unsightly and

malodorous, masses of algae can

deprive an estuary of much-needed

oxygen, interfere with swimming and
Water Quality

17

boating, and outcompete native submerged aquatic vegetation. Although algae during

periods of light produce oxygen as a result of photosynthesis, metabolic processes such as

respiration during periods of darkness and decomposition can use up dissolved oxygen in the

water column. Natural stratification exacerbates this condition and the bottom water quickly

becomes devoid of oxygen (hypoxic or anoxic). Oxygen replenishment in the bottom water

is diminished because the heavier, saltier water layer on the bottom is resistant to mixing with

the lighter, fresher water on the surface. Oxygen depletion can also occur in unstratified

waters, however. The lack of oxygen forces fish and mobile benthic invertebrates to migrate

out of an area. In extreme cases anoxia can lead to fish kills. Organisms living in the

sediments that cannot escape are variably affected as the oxygen levels decline. State and

Federal agencies monitor indicators of eutrophication in estuaries including concentrations of

nitrogen and phosphorus, chlorophyll a, reports of algal blooms, and dissolved oxygen. 

Nutrients

Nitrogen and phosphorus are the primary anthropogenic nutrient inputs of concern in coastal

waters, with nitrogen being more important in marine and estuarine systems and phosphorus

being more important in freshwater systems. Monitoring concentrations of nitrogen in

estuarine waters provides an indicator of the potential of a water body to become eutrophic. 

Although nutrients are difficult to control (primarily because they are recycled within an

estuary and often come from nonpoint sources), frequent monitoring in estuaries can serve as

an early warning in an effort to prevent eutrophication. 

The major nonpoint sources of nitrogen are fertilizer, animal manure, and atmospheric

deposition. Fertilizer nonpoint source runoff can account for up to 25% of the nutrient input

to estuaries. The highest levels of nitrogen fertilizer use (Fig. 12) in the nation occur within

the Mississippi River drainage basin.

Point sources consist mainly of wastewater treatment plants and other industries. According

to the NOAA National Estuarine Inventory (1990), the Gulf of Mexico region ranks highest

of all coastal regions in the U.S. in the number of wastewater treatment plants (1,300),

number of industrial point sources (2,000), percent of land use devoted to agriculture (31%),

and application of fertilizer to agricultural lands (62,000 tons of phosphorus and 758,000 tons

of nitrogen). 

The NOAA Estuarine Eutrophication Survey indicated that high concentrations of total

dissolved nitrogen were observed in up to 19% of the estuarine area of the gulf (Fig. 13) and

that for 8 estuaries these high concentrations were persistent year round. Rabalais (1992)

reported that out of 58 estuarine areas in the Gulf of Mexico for which information was

available, 28 had evidence of a definite or potential problem with nutrient increases. State

water quality inventories [1996 305(b) reports], indicated that the majority of estuaries in

each state were rated with acceptable nitrate concentrations. Of those estuaries in each state 
Water Quality

18

Fig. 12. Fertilizer use estimates for the United States, 1991. Data are from the USGS.

that were rated with impaired water quality, nutrients were listed as a major cause in Florida,

Louisiana, and Mississippi (Fig. 10).

Chlorophyll a

 Nutrient loading is just one indicator of the potential an estuary has to become eutrophic.

Chlorophyll a can be an indicator of the first level response to nutrient enrichment. 

Measurements of chlorophyll a in the water column represent the standing stock or biomass

of phytoplankton. Blooms of phytoplankton often indicate that an estuary is undergoing

eutrophication. In some estuaries, like Tampa Bay, there is a good correlation between

nitrogen loadings from various sources and concentrations of chlorophyll a. In other

estuaries, however, the relationship does not hold and it is possible, in fact, for an estuary to

receive heavy loads of nitrogen and yet not exhibit increases in phytoplankton biomass. 

Other factors such as light limitation, depth of the mixing zone, flushing rates, and

contaminants may affect the growth of phytoplankton. The NOAA Estuarine Eutrophication

Survey represents the only gulf-wide assessment of chlorophyll a concentrations in estuaries. 

This survey indicated that hypereutrophic (chl a > 60 g/L) conditions were observed in

seven estuaries and that high chlorophyll concentrations (20-60 g/L) were observed in 18

estuaries (Fig. 13).
Water Quality

19

Fig. 13. Concentrations of nitrogen (mg/l) and chlorophyll a (g/l) observed in estuaries of the Gulf of

 Mexico based on the Estuarine Eutrophication Survey (NOAA, 1997).
Water Quality

20

Fig. 14. Estuaries in the Gulf of Mexico with observed dissolved oxygen < 2 mg/L (marked

with red dots) on at least one sampling visit during the summer (USEPA, EMAP Database for

the Louisianian [1991-1994] and West Indian [1995] Provinces).

Dissolved Oxygen

Because dissolved oxygen (DO) is an indicator of the habitability of estuarine waters for

marine life, DO is routinely measured by monitoring programs interested in characterizing

the eutrophic state of estuaries. DO is recognized as an indicator of the extent of

eutrophication because wide fluctuations in DO often result from increased primary

productivity and may reflect prior nutrient loading. DO concentrations may also vary

because of natural processes (stratification, depth, wind-induced mixing, tidal fluxes). DO is

necessary for respiration in most aquatic animals but different biota have different

requirements for adequate DO. Hypoxia may increase stress from other factors (e.g.,

contaminants) on marine organisms, whereas anoxic conditions produce toxic hydrogen

sulfide which can be lethal to marine biota. 

Although many states require DO concentrations of 4-5 mg/L for estuaries to meet their

designated use criteria, hypoxia is often defined as DO < 2 mg/L, and anoxia as DO < 0.1

mg/L. Sufficient evidence exists that DO < 2 mg/L is extremely stressful to most aquatic

organisms. EMAP reported the occurrence of hypoxia in 10% of bottom waters of the

Louisianian Province during summer sampling from 1991 to 1994, but in only 3% of bottom

waters in south Florida in 1995 (Fig. 14). The NOAA Estuarine Eutrophication Survey

reported periodic hypoxia in 30 of 37 estuaries (25% of estuarine area) and anoxia in 16

estuaries (6% of estuarine area; Fig. 14). The apparent discrepancies between the EMAP and

NOAA assessments of hypoxia were due to programmatic differences in design and

interpretation. Low DO was usually observed from June through October and was primarily

driven by stratification of the water column.
Water Quality

21

Fig. 15. Dissolved oxygen conditions

observed in Mobile Bay, Alabama

during the summer of 1994 (Alabama

Department of Environmental

Management 1997).

Mobile Bay, the largest estuary in Alabama, is a good

example of a "Priority Hypoxia Area" identified by

Rabalais (1992). It is relatively shallow (avg. depth 3

m) with a few deep holes and a dredged shipping

channel. Mobile Bay has a historic problem with

seasonal hypoxia that often culminates in "jubilees,"

where fish and invertebrates migrate to the shore

attempting to escape low DO. Alabama's Department of

Environmental Management (ADEM) implemented an

intensive estuarine monitoring program (ALAMAP -

Coastal) in 1993. Although the extent and duration of

hypoxia in Mobile Bay varies annually, ALAMAP -

Coastal measured low DO in more than 50% of the

bottom water area in Mobile Bay during the summers of

1993 and 1994 (Fig. 15). Periodic hypoxia in Mobile

Bay is part of the natural ecology and is most often

related to salinity patterns and the degree of water

column stratification.
22
23

Fig. 16. Mixed bloom of dinoflagellates. Photo

credit: Don Anderson, Woods Hole

Oceanographic Institution.

Fig. 17. Electron photo micrograph of

Gymnodinium breve. Photo credit:

Department of Environmental Protection,

Florida Marine Research Institute.

Harmful Algal

Blooms

Microscopic, single-celled plants

(phytoplankton) serve as the primary

producers of energy at the base of the

estuarine food web (Fig. 16). Some species

of phytoplankton grow very fast, or “bloom,”

and accumulate into dense, visible patches

near the surface of the water. Although the

causes of algal blooms are not entirely

known, scientists suspect that blooms occur

as a result of a combination of high

temperatures, a lack of wind, and, frequently,

nutrient enrichment. Some algal blooms are

called brown tides, and, while not harmful to

humans, they cause serious ecosystem

impacts due to decreases in light penetration

and dissolved oxygen. Brown tides can cause

seagrass die-offs and fish kills. Some algae produce potent neurotoxins that can be

transferred through the food web, where they cause damage, even death, to animals from

zooplankton to humans.

The most well-known harmful algal bloom (HAB)

events in the Gulf of Mexico involve blooms of

Gymnodinium breve (also known as red tides; Fig.

17), which occur regularly in the fall off the coasts

of Florida and Texas. This organism discolors the

water red (although other less harmful algae can also

discolor the water red) and has been implicated in

fish kills and the deaths of manatee and other marine

mammals. G. breve produces brevetoxins that cause

Neurotoxic Shellfish Poisoning (NSP). NSP

induces gastrointestinal and neurological symptoms

in humans that, although debilitating, are not fatal. 

In addition, toxic aerosols are formed by wave

action and can produce asthma-like symptoms in

humans. This often leads to beach closures.
Harmful Algal Blooms

24

Fig. 18. Occurrence of HAB-related events in the Gulf of Mexico (National

Office For Marine Biotoxins and Harmful Algal blooms, Woods Hole

Oceanographic Institution).

Fig. 19. Red Tide bloom off the west

Florida shelf . Photo credit: Dr. Frank

Muller-Karger, University of South

Florida.

Prior to 1972, NSP and fish kills due to harmful algal blooms only occurred along the gulf

coasts of Florida and Texas in relatively localized areas. In the fall of 1996, a bloom of G.

breve spread into Alabama, Louisiana, and Mississippi waters for the first time (Fig. 18). 

Brown tides have occurred in the Laguna Madre area of the Texas coast since 1990. The

NOAA Estuarine Eutrophication survey indicated that biological resource impacts caused by

nuisance algae occur in 22 estuaries and by toxic algae in 25 estuaries in the Gulf of Mexico. 

The causes of the increase in number and

distribution of major harmful algal blooms are

unknown, but three possible explanations are

offered: (1) algal species are transferred by ballast

water from ships, (2) ocean currents deposit seed

populations, and (3) pollutants add nutrients to the

water. Many scientists believe that the G. breve

blooms in the Gulf of Mexico are a natural

phenomenon because they originate 10-50 miles

offshore in low-nutrient water (Fig. 19). This is

supported by records dating back to the 1500s of

blooms occurring offshore. Others speculate that,

although the currents in the Gulf of Mexico may

initiate a bloom with an upwelling of nutrients, the

actual bloom does not occur until the currents or

winds carry the organisms into the nutrient-rich,

shallow, near-coastal waters.
25

Fig. 20. Houston Ship Channel surrounded by

petrochemical industries and shipping activities. 

Photo credit: Galveston Bay National Estuary

Program.

Sediment

Contaminants

Toxic substances and pesticides enter Gulf of

Mexico estuaries from industrial and

municipal discharges, urban and agricultural

runoff, accidental spills, and atmospheric

deposition (Fig. 20). These activities often

have adverse effects on estuarine habitat. For

example, the U.S. Coast Guard received an

annual average of 6217 notifications of oil or

chemical spills in Gulf of Mexico ports from

1991 to 1997. Chemicals that enter estuaries

are often bound to suspended particulate

matter that eventually deposits on the

sediment surface. Sediment deposition and

accumulation rates in an estuary depend

greatly on the rate of freshwater inflow and

access to flushing from the Gulf of Mexico. 

Once deposited in the sediment, toxic chemicals may be available for uptake by benthic

organisms. Bioavailability is greatly dependent on the characteristics of the sediment,

including concentrations of total organic carbon and acid-volatile sulfide. Some chemicals

are acutely toxic, resulting in death of the animal; others may have chronic toxicity effects,

affecting growth or reproduction. Toxic chemicals can affect humans because they may

become biomagnified as they are stored in animal tissue and transferred through the food

chain. When sediment chemistry information is combined with sediment toxicity data and

benthic health indicators, a better assessment of overall sediment quality can be

accomplished.

Evaluation of the potential effects of contaminated sediments on estuarine organisms is

difficult because few applicable state or federal regulatory criteria exist to determine

"acceptable" sediment concentrations of all substances. Informal guidelines based on many

field and laboratory studies have been suggested, however. Guidelines such as effects rangelow (ER-L) and effects range-median (ER-M) values (Long et al. 1995) provide

environmental managers with benchmarks to determine if contaminated sediments have the

potential to adversely affect aquatic organisms. These (and other) guidelines benefit from the

weight of evidence afforded by large data sets associating sediment contaminant
Sediment Contaminants

26

Fig. 21. Sites where contaminants (metals or organic) exceeded Long et al. (1995) ER-L or

ER-M guidelines (USEPA, EMAP Database for the Louisianian [1991-1994] and West

Indian [1995] Provinces).

concentrations with biological effects, but suffer from a failure to incorporate the effects of

multiple chemicals in complex mixtures, as the chemicals exist in the environment. In

sediments in the Gulf of Mexico estuaries, EMAP measured polycyclic aromatic 

hydrocarbons (PAHs; components of petroleum and produced by combustion processes),

polychlorinated biphenyls (PCBs; used in insulators and capacitors), aliphatic hydrocarbons

(e.g., alkanes which are abundant in crude oil), pesticides (e.g., 

dichlorodiphenyltrichloroethane [DDT], chlordane, dieldrin, endosulfan), organotins (e.g.,

tributyltin [TBT] found in anti-fouling paint) and trace metals (e.g., zinc, lead, mercury,

cadmium, copper). EMAP reported that ER-L guidelines were exceeded for all of the major

groups of sediment contaminants, albeit at very low rates (<1% of area) for PAHs and PCBs.

There was a fairly even distribution of sites from the Florida panhandle to Corpus Christi

Bay, Texas, where contaminants exceeded ER-L or ER-M guidelines (Fig. 21). Based on the

percent area of each estuary that was contaminated, however, the majority of estuarine

systems in all gulf states were identified by EMAP as having fair to good sediment quality. 

EMAP identified several estuaries as having predominately contaminated sediments. These

correspond well with those watersheds identified by the USEPA National Sediment Inventory
Sediment Contaminants

27

Fig. 22. Location of Superfund sites near coastal areas of the gulf states (USEPA).

Fig. 23. Distribution of sites with sediment contaminants

greater than ER-L guidelines in Galveston Bay, TX (REMAP, Texas, 1993).

as “areas of probable concern.” Several USEPA Superfund sites are also located near heavily

industrialized estuaries, particularly Galveston Bay, Tampa Bay, and the Florida panhandle

(Fig. 22).

With one-half of the total chemical production and 30% of the total petroleum industry in the

U.S. located in and around Galveston Bay, Texas, this estuary provides a good example of

the impacts of urban and industrial sources on sediment quality. Galveston Bay has a history

of environmental problems as a result of rapidly escalating demands placed upon the bay’s

resources. Sediment chemistry

analyses by USEPA’s Region VI (REMAP-TX) indicated that sites in East

Bay Bayou, Trinity Bay, the marinas,

and small lakes had as many as seven

contaminants exceeding ER-L

guidelines (Fig. 23). In East Bay

Bayou, several PAHs, including

fluorene and phenanthrene, exceeded

ER-L guidelines. At the marinas and

in Offats Bayou, copper and

chlordanes exceeded ER-L values. 

Offats Bayou also had high levels of

lead, zinc, and DDT.
29

Fig. 24. Total acreage of dominant coastal wetland types by state based on U.S. Fish and Wildlife Service

wetland inventory maps (NOAA, 1991).

Habitat Change

Wetlands

Wetlands are the interface between the aquatic and terrestrial components of estuarine

systems. In the Gulf of Mexico, wetlands include both emergent (i.e., marshes and certain

forested scrub-shrub habitats) and submerged vegetated habitats (seagrasses; Fig. 24). These

habitats are critical to the life cycles of fish, shellfish, migratory birds, and other wildlife;

they also filter and process residential, agricultural, and industrial wastes, thereby improving

surface water quality, and they buffer coastal areas against storm and wave damage. An

estimated 95% of commercial fish and 85% of sport fish spend a portion of their lives in

coastal wetland and estuarine habitats. Adult stocks of commercially harvested shrimp in the

Gulf of Mexico are directly related to wetland quality and quantity (Turner and Boesch,

1988). Wetlands in the Gulf of Mexico region are being rapidly damaged or destroyed by

human activities (e.g., flood control, agriculture, waste disposal, real estate development,

shipping, commercial fishing, and oil and gas exploration and production) and natural
Habitat Change

30

Fig. 25. Estimated total area of wetlands by state in 1780

and 1980 (Dahl, 1990; U.S. Fish and Wildlife Service).

processes (e.g., rising sea level, sediment compaction and submergence, droughts, animal

"eat-outs," storms, and floods; Table 1).

Table 1. Primary causes of diminishing quality and acreage of coastal emergent

wetlands in the Gulf of Mexico by state (Duke and Kruczynski, 1992).

State Cause

Texas Subsidence due to extraction of oil, gas, and fresh water

Louisiana Navigation channels altering hydrodynamic flow

Natural subsidence

Reduced sediment deposition

Mississippi Dredge and fill operations

Alabama Dredge and fill operations

Florida Conversion to commercial and private developments

Total existing coastal wetland acreage and historical wetland loss estimates are the most

frequently cited indicators of wetland status. In a pilot study EMAP evaluated additional

indicators of wetland health that included the condition of individual plant species and soil

characteristics, in addition to acreage and loss estimates. These indicators were not measured

gulf-wide, however, and were not used for assessment in this report. Discrete estimates for

wetland acreage or loss for estuaries in the Gulf of Mexico were not available. Where

information on coastal wetland loss was available (e.g., for Louisiana) it was used; otherwise,

total wetland loss estimates were gathered for each gulf state. Total wetland loss (coastal and

inland) for the five gulf states from 1780 to 1980 was estimated to be 40 million km2 

(approximately 50%; Fig. 25). Although agriculture is the leading cause of all wetland

losses, including coastal and inland, residential and commercial development accounted for

42% of estuarine wetland loss nationwide from 1985 to 1995. Between 1985 and 1995 the

southeastern U.S. lost the greatest area of wetlands (51% of national total), but the rate of

wetlands loss both nationally and in the gulf has slowed considerably. 

Coastal emergent wetland loss for

Louisiana represents 67% of the

nation's total loss (177,625 ha or

438,911 acres) from 1978 to 1990

(Fig. 26). Much of this loss is related

to altered hydrology stemming from

navigation, flood control, and mineral

extraction and transport projects. 

Most actual wetland loss is the result

of the indirect effects of these

projects, specifically the disruption of

flow and natural movement of water

and sediments rather than actual loss

due to erosion.
Habitat Change

31

Fig. 26. Changes in wetland area for coastal Louisiana based on National Wetland Inventory data and

Landstat TM Imagery compiled by USGS Baton Rouge Project Office.

Submerged Aquatic Vegetation

Submerged aquatic vegetation (SAV) species, or seagrasses, are particularly sensitive to light

and water quality. Seagrasses have an important ecological role in providing food for

waterfowl, manatees, and green sea turtles, and in providing habitat for many fish and

shellfish species. SAV also affects physical processes in estuaries, such as nutrient cycling,

sediment stability, and water turbidity. Changes in seagrass distribution, therefore, can

reflect the health of an estuary, and losses of seagrasses may be an indicator of water quality

problems. Seagrass habitat loss ranges from 20% to 100% over the last 50 years for most

estuaries in the northern Gulf of Mexico (Handley, 1995). This decline is related primarily to

coastal population growth and accompanying municipal, industrial, and agricultural

development, but some losses may also be attributed to natural causes (i.e., hurricanes,

storms, and salinity changes). Currently, 95% of the seagrass acreage in the Gulf of Mexico

is localized in estuarine areas of Florida and Texas. The NOAA Estuarine Eutrophication

Survey reported that the spatial coverage of SAV was very low to low (>0 to 25% coverage)

in 32 estuaries, particularly in the mixing zone. Spatial coverage was high in Apalachee Bay,

Florida and Laguna Madre, Texas. NOAA estimated that the spatial coverage of SAV in the

gulf was equivalent to 12-24% of the estuarine area. Where trends in SAV coverage were

observed, both increasing and decreasing trends were attributed to habitat alteration or to

changes in nonpoint and point sources of pollution and in hydrology.
33

Fig. 27. Percent area of estuaries in the

Louisianian Province classified by the benthic

index as degraded (< 3), moderate (3-5), or

reference (> 5) (USEPA, EMAP Database for the

Louisianian Province, 1991 to 1994).

Biological 

Integrity

Changes in biological communities may indicate a disruption of healthy environmental

conditions. Quantifying the condition of biological communities enables us to identify the

cumulative effects of pollution or habitat alteration. EMAP-E uses biological monitoring of

benthos and fish to evaluate estuarine condition. The National Marine Fisheries Service

(NMFS) monitors the productivity of fisheries to ensure the economic health of the fishing

industry. The U.S. Fish and Wildlife Service (USFWS) is responsible for tracking the

population status of waterfowl, which is an important indicator of wetland condition. 

Monitoring the recovery of threatened and endangered species provides important

information about the success of management actions designed to protect the habitat of those

species.

Benthos

The worms, clams, and crustaceans that

inhabit the bottom substrates of estuaries are

collectively called benthic macroinvertebrates

or benthos. These organisms play a vital role

in maintaining sediment and water quality,

and are an important food source for bottomfeeding fish, shrimp, ducks, and marsh birds. 

Benthos are often used as indicators of

perturbations in the estuarine environment

because they are relatively nonmobile, and

therefore cannot avoid environmental

problems. The response of benthic

communities to alterations in sediment and

water quality is relatively well understood and is often expressed as changes in community

structure, density, and diversity. Benthic population and community characteristics are

sensitive indicators of contaminant and dissolved oxygen stress, salinity fluctuations, and

disturbance and serve as reliable indicators of estuarine environmental quality. EMAP-E

developed a benthic index of environmental condition for estuaries that incorporates changes

in diversity and the populations of indicator species to distinguish degraded benthic habitats

from undegraded benthic habitats (Engle et al. 1994; Engle and Summers 1999). Using the

benthic index, 25% of the estuarine area in the Louisianian Province was determined to have
Biological Integrity

34

Fig. 28. Areas in Pensacola Bay, Florida that were classified by the benthic index as

degraded (s), moderate (s ), or reference (s) (Engle and Summers, 1998).

degraded benthic resources from 1991 to 1994 (Fig. 27) (Macauley et al. 1999). When

examined on the level of an individual estuary (e.g., Pensacola Bay, FL), degraded benthic

resources were most often associated with sediment contaminants or hypoxia (Engle and

Summers 1998).

Pensacola Bay, an estuary in northwest Florida, has a sedimentation problem because of poor

flushing and high suspended sediment input from its tributaries. Evidence of problems in the

bay include low benthic diversity, decline of seagrasses and oyster populations, and

contaminated sediments, especially in the bayous. Pensacola Bay has predominantly muddy

sediments, dominated by polychaete and nemertean worms that are, in general, tolerant to

habitat disturbances. The benthic index identified 12 degraded sites located primarily in the

mainstem of Pensacola Bay and in the three bayous near Pensacola (Bayous Chico, Grande,

and Texar) (Fig. 28). Areas of Pensacola Bay have severely contaminated sediments, with as

many as 40 chemicals at concentrations greater than ER-L guidelines, especially in the

bayous. The benthic community is severely impoverished in the areas of the bay with low

sediment quality. 
Biological Integrity

35

Fig. 30. Landings by weight and value of all

commercial species by state in the Gulf of Mexico in

1996 (National Marine Fisheries Service).

Fig. 29. Landings in 1996 by weight and value for

the top four commercial species in the Gulf of

Mexico (National Marine Fisheries Service).

Commercial and Recreational Fisheries

There is much public concern about the quality and abundance of fish, especially

commercially and recreationally important species. Estuaries provide food, refuge from

predation, and habitat for a wide variety of fishes and invertebrates. Many of these species

are economically important and use various estuarine habitats to complete their life cycles. 

Estuaries are especially important as nursery areas for many species during their early and

juvenile life stages. As a result, the economic viability of the commercial and recreational

fisheries of the Gulf of Mexico is also estuarine dependent. Tracking the status of fishery

resources is one step in the effort to build sustainable fisheries. The decline of fisheries may

be due to overfishing or habitat degradation. As the carrying capacity of an estuary declines,

the fish stocks which inhabit it can no longer support fishing levels that were previously

sustainable. Therefore, the status of fishery resources can be used as an indicator to assess

the suitability of estuarine habitat for sustaining those fisheries. The top four fisheries in the

Gulf of Mexico (menhaden, shrimp, oyster, blue crab) use estuaries extensively (Fig. 29). 

The Gulf of Mexico yielded the nation's largest regional commercial fishery (excluding

Alaska) by weight in 1996, representing 33% of the national total by weight and 32% by

value. The total commercial harvest in the Gulf of Mexico was dominated by the landings

from Louisiana (Fig. 30). The Gulf of Mexico shrimp fishery is the largest and most valuable

in the United States, accounting for 69% of the total domestic harvest, with most of the

shrimp landings in Louisiana and Texas (Fig. 31). Shrimp are especially dependent on

estuaries, and the degradation of estuarine water quality and loss of gulf wetlands are

considered significant threats to this fishery. 

Recreational fishing is also important to the economy of gulf states. Over 40% of the nation's

marine recreational fishing occurs in the Gulf of Mexico, with the highest number of anglers

fishing in Florida and Texas (Fig. 32). Although many of the recreational fish species are

exclusively offshore, some use estuaries for a major part of their life cycle. Speckled trout

(or spotted seatrout; Cynoscion nebulosus), for example, spawns over seagrass beds but is

known to migrate offshore and red drum (Sciaenops ocellata) spawns in estuaries where the
Biological Integrity

36

Fig. 31. Landings of shrimp by state and species in

the Gulf of Mexico in 1996 (National Marine Fisheries

Service).

Fig. 32. Numbers in thousands of recreational

anglers fishing in coastal waters in 1995 by state

in the Gulf of Mexico (National Marine Fisheries

Service; Texas Parks & Wildlife).

Fig. 33. Commercial landings of red drum by weight and

value in the Gulf of Mexico from 1950 to 1995 (National

Marine Fisheries Service).

young develop for 2-3 years before moving offshore. 

The Red Drum Fishery

The drums (Family Sciaenidae) are characteristic of inshore fishes found in the northern Gulf

of Mexico and include important commercial and recreational species such as red drum (or

redfish), black drum (Pogonias cromis), spotted seatrout, and Atlantic croaker. Most species

spawn in shallow offshore waters or at the entrance to a bay; the larvae enter estuaries, where

they spend one or more summers and take advantage of the greater availability of food and

protection which estuarine habitats afford. Some species, such as red and black drum, are

long-lived.

The red drum commercial fishery was closed to all harvest in U.S. Federal waters of the Gulf

of Mexico on January 1, 1988 (Fig. 33). Stock assessments indicated that red drum were

heavily fished prior to moving offshore to spawn and that those fish less than 12 years of age

were poorly represented in the

offshore spawning population. In

addition to the federal closure, states

enacted stringent measures to reduce

red drum mortality in inshore areas. 

Red drum populations appear to be

responding to the management

measures, and, although all five

states have recreational bag limits

and slot limits that exclude large fish,

Texas has issued “Red Fish Tags”

that allow anglers to keep two large

fish per year.
Biological Integrity

37

Fig. 34. Commercial landings of black drum by weight

and value in the Gulf of Mexico from 1950 to 1995

(National Marine Fisheries Service).

Fig. 35. Distribution by species of the 408 fish with observed

gross pathological disorders (USEPA, EMAP Database for the

Louisianian Province, 1991 to 1994).

Following the federal closure and

state regulatory actions on red drum,

black drum were accepted as a

substitute within the commercial

market (Fig. 34). This "new" fishery

added to the already existing pressure

on black drum and led the gulf states

to establish interim regulatory

measures. As a result, present harvest

levels are well below those which are

thought to negatively affect

recruitment and spawning stocks.

Fish Biomarkers

An increased awareness of the adverse effects of environmental degradation on fish

populations has led many federal and state monitoring programs to include fish health

assessment (Blazer et al. 1994). Fish from contaminated waters often display pathological

conditions such as fin rot, skin ulcerations, skeletal abnormalities and epidermal growths. In

addition, these abnormalities may be indicators of health risk to birds, mammals, and even to

humans. Therefore, as an indicator of environmental conditions, fish abnormalities should

be of interest to resource and regulatory agencies as well as to the general public. Fish

biomarkers such as gross pathology, splenic macrophage aggregates, and skeletal anomalies

were investigated by EMAP in the Gulf of Mexico from 1991 to 1994.

The frequency and type of gross pathologies on fish taken from trawls in estuarine waters are

indicators of the overall condition of fish populations. Field and laboratory studies have

shown an association between gross pathological disorders in fish and exposure to pollution. 

Gross pathological disorders in fish

include tumors and lesions on the

skin, malformations of the eye, gill

abnormalities, and parasites. From

1991 to 1994, in the Louisianian

Province, EMAP examined 64,082

fish caught in trawls for external

gross pathological disorders. Gross

pathologies were observed on 408

fish, which gives a background

pathology incidence rate of 0.6%. 

Of all pathologies observed, 61%

were parasites and 45% occurred in

menhaden (Brevoortia patronus; 

Fig. 35). The majority of observed

pathologies (88.8%) occurred in
Biological Integrity

38

Fig. 36. Sites in the Gulf of Mexico where fish samples contained spleens with > 40 macrophage aggregates

per mm2

 (USEPA, EMAP Database for the Louisianian Province, 1991 to 1994).

Texas and Louisiana, with 47% of all pathologies found in fish from Galveston Bay, Texas. 

Gross pathological abnormalities were more prevalent at sites with high sediment

contaminant concentrations (Fournie et al. 1996.)

Macrophage aggregates are a prominent feature of fish spleen, kidney, and liver. Recent

studies suggest that the size and density of macrophage aggregates may be sensitive

histological indicators of fish health and environmental quality (Blazer et al. 1994). 

Although macrophage aggregates have been criticized as nonspecific, there is some evidence

that, when demersal fish are examined, increased size and density of macrophage aggregates

are associated with environmental contamination. One hundred ninety-one fish samples from

149 sites were examined for macrophage aggregates by EMAP-E from 1992 to 1994. Fish

from only five of these samples contained spleens with more than 40 macrophage aggregates

per square millimeter (Fig. 36). This incidence of relatively high macrophage aggregate

density represents a small percentage of the total number of fish examined indicating a

localized effect of pollution on fish.

Coastal and Marine Birds

Gulf of Mexico estuaries provide necessary habitat for both migrant and resident coastal and

marine birds. Waterfowl, primarily ducks and geese, migrate to Gulf of Mexico feeding

grounds during winter to take advantage of the vast estuarine resources. Canvasback

(Aythya valisineria), redhead (Aythya americana), and scaups (Aythya spp.) and other divers

such as the ruddy duck (Oxyura jamaicensis), feed and congregate in open waters of
Biological Integrity

39

Fig. 38. Breeding populations of wading birds and

seabirds common to the gulf coast showing the percent of

population located among the gulf, Florida, and Atlantic

coasts (U.S. Fish and Wildlife Service, 1988).

Fig. 37. Estimates of the number of redhead

ducks in the North American breeding population

from 1950 to 1996 (Smith, 1995; Federal Duck

Stamp, 1987-1988).

estuaries, often clustered in dense rafts. An

estimated 80% of the redhead population

overwinters in the brackish to hypersaline

waters of Laguna Madre, Texas. Other

redhead wintering grounds in the Gulf of

Mexico include Chandeleur Sound, Louisiana

and Apalachee Bay, Florida. Redheads are

especially dependent on healthy SAV beds in

their wintering areas. If the decline in SAV

continues (over 50% of shoalgrass beds in

Laguna Madre have disappeared since the

1960's), the redheads may be forced to find

new wintering grounds. Healthy and stable

populations of waterfowl are indicators of

healthy estuarine and wetland conditions in

the Gulf of Mexico. Although redheads declined below their target population size of

760,000 during the 1980's, redheads currently exceed their target population size (Fig. 37).

Wading birds of the coastal Gulf of

Mexico include the families, Ardeidae

(herons, egrets and bitterns),

Ciconiidae (storks), Gruidae (cranes),

and Threskiornithidae (ibis and

spoonbills). The most abundant

species in estuaries are tricolored

herons (Egretta tricolor) and snowy

egrets (Egretta thula). More than 80%

of the total number of breeding

tricolored and little blue herons

(Egretta caerulea) nest along the gulf

coast. Although the number of

colonies of wading birds on the gulf

coast is often less than the number of

colonies on the Atlantic Coast, the gulf

colonies are larger in number of birds,

accounting for a majority of the total

breeding population of wading birds

(Fig. 38). The wading birds listed in

Figure 38 prefer salt marshes and

other wetlands bordering coastal bays. 

The North American Breeding Bird

Survey summarizes trends in wetland

breeding birds (e.g., herons) from

1966-1996. Significant decreasing
Biological Integrity

40

Fig. 39. Illustration of a Gulf sturgeon.

trends in little blue heron populations were indicated for Alabama and Florida, while

significant increasing trends for other wading birds were indicated for all of the gulf states.

The most common marine birds along the gulf coast include laughing gulls (Larus atricilla),

terns (sub Family sterninae), and migrating sandpipers (Family Scolopacidae) and plovers

(Family Charadriidae). Laughing gulls are the only gull species that nest on the gulf coast,

and are the most abundant marine birds to nest in this region. The largest populations of

black skimmers (Rynchops niger) and gull-billed terns (Sterna nilotica) in the U.S. nest along

the gulf coast (Fig. 38). These birds utilize almost exclusively coastal bays and nearshore

waters for both nesting and feeding. The North American Breeding Bird Survey had little or

no trend information for these marine birds in the gulf states, however, laughing gulls were

listed as showing a significant increase in population from 1966-1996 in the southeast.

Threatened and Endangered Species

Degraded water quality, altered water flow, and loss of suitable habitat are the greatest threats

to aquatic species at risk of extinction. Efforts to minimize water pollution or restore natural

flow should contribute to the protection of threatened or endangered species. Because these

species are already at risk, they act as sentinels, providing us with early warnings of even

small perturbations in their environment. Charting their recovery also provides us with an

indicator of the success of management programs designed to ensure that these species have a

clean and safe habitat. 

The Gulf sturgeon (Acipenser oxyrhynchus desotoi; Fig. 39) was listed as a threatened

subspecies on September 30, 1991. The Gulf sturgeon is an anadromous fish, migrating from

salt water into large coastal rivers. Historically, the Gulf sturgeon occurred in rivers from the

Mississippi River to the Suwannee River and in bays and estuaries from Florida to Louisiana. 

Little is known about current population levels outside the Suwannee, Apalachicola and Pearl

Rivers but they are thought to have declined from historic levels. Although much of the

sturgeon’s life is spent in fresh water, it utilizes bays and estuaries for feeding and migration. 

Major threats to this rare, primitive species include physical barriers (e.g., locks and dams) to

spawning grounds, habitat loss, and poor water quality.
Biological Integrity

41

Fig. 40. Photograph of two manatee. Photo credit:

Homosassa Springs State Wildlife Park.

Fig. 41. Photograph of adult brown pelican. 

Photo credit: Marcus G. Martin, University of

Minnesota.

The Florida manatee (Trichechus

manatus; Fig. 40) is currently listed as

an endangered species, although

ongoing efforts to protect manatee have

been successful and the Florida

population appears to be rebounding. 

Manatee inhabit freshwater, brackish,

and marine waters throughout the gulf

coast, although the largest population is

in Florida. Along the gulf coast of

Florida, the principal summer habitats

of manatee are estuaries and riverine

grassbeds where they feed on

submerged, emergent, and floating

vegetation. Because manatee depend

on healthy estuarine habitat, shifts in

population counts may indicate

degradation of the coastal environment. The greatest human impacts on manatee survival

include recreational boat traffic and intensive coastal development, but some manatee

mortalities may also be attributed to natural causes (e.g., cold temperatures or red tide). In

1996, a record number of manatee (2,639) were counted in the January survey, but a record

number of deaths also occurred (416), with 151 deaths attributed to toxic red tide and 60 to

watercraft. The U.S. Fish and Wildlife Service’s first 1997 survey reported an encouraging

population count of 2,229 manatee with a record high 1329 on the Florida west coast despite

the 1996 red tide deaths.

The brown pelican (Pelecanus occidentalis;

Fig. 41) is still listed as endangered in

Louisiana, Texas, and Mississippi, while stable

populations now thrive in Florida and Alabama. 

Brown pelicans nest in colonies along the gulf

coast and feed primarily on fish from shallow

waters of estuaries. Because they depend on

high quality coastal habitat, declining trends in

brown pelican nesting populations may indicate

degradation of nesting substrate or fluctuations

in food supply. Brown pelican populations

declined sharply in the 1950's and 1960's,

primarily due to the ingestion of fish

contaminated with pesticides like DDT. In the

1970's, the banning of DDT and listing the

pelican as an endangered species contributed to its successful rebound. The gulf coast

population, while still considered endangered, was recently estimated at 6,000 breeding pairs.
Biological Integrity

42

Fig. 42. Photograph of a baby Kemp’s ridley sea turtle. 

Photo credit: Bill Reaves, Texas Parks and Wildlife

Department.

Several sea turtles are listed as

endangered in the Gulf of Mexico,

including the Kemp’s ridley

(Lepidochelys kempii; Fig. 42),

green (Chelonia mydas),

loggerhead (Caretta caretta),

leatherback (Dermochelys

coriacea), and hawksbill

(Eretmochelys imbricata). Adults

of the Kemp’s ridley sea turtle are

restricted to the Gulf of Mexico,

where their major non-nesting

habitat includes nearshore and

inshore waters (especially in

Louisiana) and salt marshes where

they feed on crabs and other

invertebrates. The entire

population of Kemp’s ridley sea turtles has expanded its nesting range beyond the 5 miles of

beach in Tamaulipas, Mexico. In 1947 the population was estimated at 42,000 females;

currently, an estimated 1500 females return to nest and their numbers have been declining

each year. Major threats to this turtle have included overharvesting, shrimp nets, oil spills,

marine debris, and dredging. Currently the Mexican government has banned harvest of

Kemp’s ridleys and instituted strict management and protection efforts while the National

Marine Fisheries Service has implemented regulations that require shrimp fisherman to use

turtle excluder devices in their trawls.
43

Fig. 43. Classified shellfish - growing waters in

thousand acres in the Gulf of Mexico (NOAA,

National Ocean Service).

Public Health

Many pollutants found in Gulf of Mexico waters have the potential to produce acute and chronic

human health effects. Humans may be exposed to waterborne toxins or pathogens via two principal

pathways: consumption of fish and shellfish and direct contact with water. The degree of human

health risk depends upon the specific characteristics of the pollutant, including its potential to reach

and thereby cause adverse impacts in humans. As an example, an advisory was issued by the

Louisiana Department of Health and Hospitals in June 1997 for Lake Pontchartrain. This advisory

was for swimming, consuming, inhaling spray or otherwise contacting the water after a toxic

cyanobacterial bloom spread over the lake following the opening of a spillway from the Mississippi

River.

Shellfish - Growing Waters 

Shellfish resources in Gulf of Mexico estuaries range from those located only in brackish water to

those found mainly in salt marshes and inshore coastal areas, and include penaeid shrimp (Penaeus

spp.), blue crab (Callinectes sapidus), and oysters (Crassostrea virginica). Oysters are important

ecologically because they have a major role in altering water clarity through filter-feeding and

because oyster reefs are vital habitats for other species. The Gulf of Mexico is the largest oysterproducing region in the Nation, with 57% of the national total in 1996.

Shellfish-growing waters in the Gulf of

Mexico refer mainly to oyster-producing

waters. These are affected by urbanization

and may be closed to harvest because of

pollution. The National Shellfish Sanitation

Program (NSSP) classifies shellfish-growing

waters to protect public health. Shellfishgrowing waters are classified as approved,

conditionally approved, restricted, or

prohibited based on sanitary surveys that

identify actual pollution sources and evaluate

water quality data (Fig. 43). In cases where

water quality problems are the cause of

shellfish bed closures, this indicator could be

used to determine the area and extent of pollution. The acreage of shellfish-growing waters that are

harvest-restricted because of pollution can be used as an indicator of water quality to measure the

progress of improved coastal zone management efforts. Although the gulf region contains the most

classified shellfish-growing waters in the nation (6.3 million acres in estuaries in 1995), it also ranks

first in total acres of prohibited shellfish-growing waters. From 1990 to 1995 the total acres of

approved shellfish-growing waters decreased by 574,000 acres (Fig. 43). The top three pollution

sources affecting harvest limitation in 1995 were upstream sources, individual wastewater treatment
Public Health

44

Fig. 44. Commercial landings of oyster in the Gulf of Mexico by state from 1950 to 1995 (National

Marine Fisheries Service).

plants, and wildlife. Commercial landings of oysters decreased from 1985 to 1990 but have

increased since 1990, especially in Louisiana and Texas (Fig. 44).

Contaminants in Fish and Shellfish

Seafood consumption advisories are designed to protect the public from the health risks of

consuming contaminated fish and wildlife. These advisories serve as a warning that high

concentrations of harmful chemicals (e.g., mercury and dioxins) have been found in local fish and

wildlife. Consumption advisories are useful as a benchmark because the number of waterbodies

added to the list each year is frequently a direct indicator of increasing environmental contamination. 

As of 1997, Florida, Alabama, Louisiana, and Texas had fish consumption advisories in effect for

selected estuarine waters (Table 2).

Other federal monitoring programs that track the occurrence of chemicals in fish and shellfish tissue

include EMAP and the NOAA National Status and Trends Program Mussel Watch Project. Analysis

of chemical contaminants in the edible tissue of fish and shellfish provides information on the

bioaccumulation of contaminants released to the environment. This information could provide an

early warning for emerging problems that could affect the viability of estuaries. Guidance values

(U.S. Food and Drug Administration or international) for metal concentrations were exceeded in

catfish, croaker, and shrimp tissues analyzed by EMAP. In most cases, however, only a low

percentage of the fish populations showed elevated concentrations of trace metals (Fig. 45), and none

showed elevated levels of either pesticides or PCB’s. The high concentrations of arsenic in catfish

(Fig. 45) may be an artifact of the chemical analysis that did not separate organic forms of arsenic

from inorganic forms. The NOAA Mussel Watch Project identified increasing trends, however, in

the concentrations of at least one target contaminant in oyster tissue from 21 of 55 monitored sites in

the gulf. Only six sites with increasing trends also had high concentrations of one or more metals.
Public Health

45

Advisory Location Pollutant Species Population affected1

Florida marine waters Mercury shark Restricted—general

Restricted—special

Gulf of Mexico, FL Mercury King mackerel 33-39" Restricted—general

Restricted—special

King mackerel > 39" No consumption—general

Charlotte Harbor, FL Mercury Spanish mackerel,

crevalle jack, spotted

seatrout

Restricted—general

Restricted—special

Tampa Bay, FL Mercury gafftopsail catfish,

crevalle jack, ladyfish,

Spanish mackerel

Restricted—general

Restricted—special

Florida Keys, FL and Florida

Bay, FL

Mercury crevalle jack and spotted

seatrout

Restricted—general

Restricted—special

Alabama Coastal Waters Mercury King mackerel >39" No consumption—general

King mackerel <39" Restricted—general

No consumption—special

Bayou D'Inde, LA PCB’s

Hexachlorobenzene

Hexachlorobutadiene

fish and shellfish Restricted—general

Calcasieu River PCB’s

Hexachlorobenzene

Hexachlorobutadiene

fish Limited consumption

Gulf of Mexico - off of LA

Coast

Mercury King mackerel  39" Restricted—general

Restricted—special

King mackerel > 39" No consumption—general

Lavaca Bay, TX Mercury fish and crab Fishing ban

Houston ship channel, TX

Upper Galveston Bay, TX

Dioxins catfish and blue crab No consumption—special

Restricted—general

Gulf of Mexico, TX Mercury King mackerel Restricted—general

Restricted—special 1

 Terms for Population Affected:

Restricted - consumption should be limited to one meal per week; this varies by state

No consumption - fish should not be consumed at all by the population affected

General - population, in general

Special - population, special high-risk groups (e.g., children and women of child-bearing age)

Table 2. 1997 Active Fish Consumption Advisories for Gulf of Mexico Estuarine Waters (USEPA 1997).
Public Health

46

Fig. 46. Number of fish kill events and number of fish

killed in Gulf of Mexico coastal waters from 1980 to 1989

(NOAA/ORCA 1991).

Fig. 45. Percent of sampled population for

target species with tissue concentrations of

metals that exceeded FDA guidelines (USEPA,

EMAP Database for the Louisianian

Province, 1991 to 1994).

Fig. 47. Percent of all fish kill events

in Gulf of Mexico coastal waters from

1980 to 1989 that were caused by low

dissolved oxygen, temperature,

storms, or waste water

(NOAA/ORCA 1991).

Fish Kills

The assessment of mortalities of fish, or fish kills, can

be used by environmental managers to determine

areas of concern. Large numbers of dead or dying

fish in estuaries are an aesthetic nuisance as well as a

health threat. Fish kills may be indicators of natural

phenomena like sudden changes in temperature

(“freeze kills”), oxygen depletion resulting from

sustained periods of hot weather coupled with lowflow conditions, or red tide. Human activities such as

accidental toxic chemical spills, toxins released in

wastewater, or nutrient enrichment may also

contribute to fish kills. Most states are mandated to

respond to fish kill events, to determine the most

probable cause, and to compile summaries

of fish kills. NOAA compiled a nationwide

database of fish kills in coastal waters from

1980-89. Results indicated that there was

no trend in fish kill events during this time

(Fig. 46), but that the majority of fish kill

events occurred during the summer months

and were caused by hypoxia (Fig. 47). A

national “hot spot” for fish kills was in

Texas, where Galveston County had the

highest number of fish killed and Galveston

Bay had the most reported events. 

Currently, an association of Federal and

State agency personnel are creating a

network for Gulf of Mexico coastal waters

to report fish kill events (Gulf of Mexico

Aquatic Mortality Network or GMNET). 

GMNET’s mission is (1) to enhance

cooperation among the Gulf states so that fish kill data

are collected and reported in a timely and consistent

manner, and (2) to determine if fish kill events can be

used as an indicator of environmental perturbation in

estuaries.
47

Ecological

Report Card

In a letter addressed to participants attending a National Environmental Monitoring and

Research Workshop at the Smithsonian Institution on September 25, 1996, Vice-President

Gore challenged federal agencies to “work with the scientific community and other interested

parties to produce a ‘report card’ on the health of our Nation's ecosystems by 2001. This

report card should establish an environmental baseline to evaluate the status of our

ecosystems.” Partly in response to this challenge, EMAP’s research strategy includes

regional-scale geographic assessments that will result in “State of the Region” reports. 

Geographic assessments will use ecological indicators to describe the status and trends in the

condition of environmental resources within a region and to evaluate the probable causes of

the observed effects.

This report takes one step in assessing the health of Gulf of Mexico estuaries. This

assessment may serve as a baseline for conditions in gulf estuaries. Progress to date can be

estimated and the effects of future management decisions can be gauged by comparing future

conditions to the data presented in this report. 

The rating of each indicator is summarized separately using a green to red (rank scores of 1 to

5) color scheme where green means good or no problem, and red means poor or severe

problem. Where possible, rankings were based on the percent area of estuaries that were

affected by levels of one or more indicators that described “problem” conditions (see final

report card at the end of this chapter for a key to the color scheme). 

Nutrients FL AL MS LA TX Gulf

Eutrophication is potentially one of the most critical problems facing gulf coastal ecosystems. 

Excess nitrogen enters gulf estuaries via fertilizer runoff from agricultural and residential

land, animal manure, and atmospheric deposition. The gulf region has the highest number of

wastewater treatment plants and the most land devoted to agriculture with the most applied

fertilizer. Many gulf estuaries show evidence of pre-eutrophic or eutrophic conditions. The

goal of State and Federal agencies responsible for managing coastal ecosystems is to identify

potential problems and take preventive actions before they become a reality. Four indicators

of nutrient enrichment were used to assess the overall nutrient status of estuaries: the NOAA

Estuarine Eutrophication Survey, state 305(b) assessments of nitrogen and chlorophyll levels,

and Rabalais’ (1992) evaluation of nutrient increases. Nutrient problems ranged from

minimal in Alabama to definite problems in Louisiana and Texas with overall moderate
Ecological Report Card

48

problems throughout the gulf.

Dissolved Oxygen FL AL MS LA TX Gulf

Dissolved oxygen (DO) in the Gulf of Mexico has received much press recently due to the

large area of hypoxia located on the continental shelf off the Louisiana coast. Estuarine

hypoxia, on the other hand, is less understood except at a local level (e.g., the “jubilee”

phenomenon in Mobile Bay). Low DO in estuaries may be attributed to natural cycles of

stratification, metabolism, seasonal storm events, and depth/tide regimes. Low DO is often

exacerbated by the anthropogenic effects of nutrient enrichment habitat modification, and

channelization. Using EMAP and NOAA data and Rabalais’ (1992) assessment of oxygen

depletion, gulf estuaries ranked as fair overall, with most of the estuaries with persistent low

DO occurring east of the Mississippi River.

Sediment

Contaminants FL AL MS LA TX Gulf

Long et al.’s (1995) ER-L and ER-M values provide guidance for environmental managers to

identify sediments with a possible or probable likelihood of causing adverse effects to the

biota. Using these and other guidelines in an assessment of contaminants in gulf estuaries,

Engel and Evans (1997) concluded that “the coastal Gulf of Mexico is not broadly at risk

from persistent chemical contaminants.” We compared the EMAP data to these guidelines

and also concluded that estuarine sediments in the Gulf of Mexico, are in fair condition

overall with respect to contaminants. The few “hot spots” that have been identified by largescale monitoring programs seem to be localized to shipping channels and point sources. 

Wetlands FL AL MS LA TX Gulf

We were unable to obtain standardized data on coastal wetland loss rates throughout the Gulf

of Mexico region. The National Oceanic and Atmospheric Administration reported in 1991

that although the gulf had the most acreage of coastal wetlands in the United States, the

region also had the highest rate of wetland loss. Total loss of wetlands (coastal and inland) in

the gulf states ranged from 41% in Louisiana to 54% in both Florida and Mississippi from

1780 to 1980. Seagrass habitat loss ranged from 20% to 100% for most gulf estuaries over

the past 50 years. The acreage of coastal wetlands has continued to diminish since the 1950's

in all states, although the rate of wetland loss has slowed (e.g., from 42 mi2/yr during the

1970's to 25 mi2

/yr in the 1990s in Louisiana). Most coastal wetlands are lost to residential

and commercial development although, in Louisiana, coastal wetlands are often destroyed by

hydrologic alterations. The high rate of coastal wetland loss in the Gulf of Mexico is mostly

the result of man’s influence.

Benthos FL AL MS LA TX Gulf

EMAP-E collected benthic samples from northern gulf estuaries from 1991 to 1994. A

benthic index of estuarine condition was developed by EMAP-E that can be used to indicate

whether the benthic communities are similar to known degraded communities, known

reference communities, or are somewhere between these two extremes. Twenty-three percent

of the estuarine area in the northern Gulf of Mexico (excluding Tampa Bay to Florida Bay)

had degraded benthic communities. When the condition of the benthos is examined on a
Ecological Report Card

49

local level, degraded benthic communities are often associated with sediment contaminants

or hypoxia.

Fish/Shellfish

Landings

FL AL MS LA TX Gulf

The top four fisheries in the Gulf of Mexico (menhaden, shrimp, oyster, blue crab) use

estuaries extensively. Trends in commercial landings vary among the gulf states but are, in

general, stable. The shrimp fishery in the gulf, for example, accounts for 69% of the

domestic harvest of shrimp. Shrimp landings are stable in Florida, Alabama, and Mississippi,

but they have been decreasing in Louisiana and Texas. Degraded water quality and loss of

wetlands have been cited as possible causes of the declines in shrimp fisheries in these states. 

A fishery management success story can be seen in the history of the red drum. Following a

severe population crash due to overfishing in the late 1980's, the red drum fishery was closed

to all commercial harvest. A decade later, however, the red drum population in the gulf is

recovering, and limited fishing is now allowed in all gulf states.

Fish Biomarkers FL AL MS LA TX Gulf

Fish health assessments were made by EMAP-E in the northern gulf estuaries (excluding

Tampa to Florida Bay) by examining fish for gross pathological disorders and splenic

macrophage aggregates. Incidences of fish pathologies and macrophage aggregates occurred

at a higher rate in Alabama and Texas than in the other gulf states but were, in general,

confined to certain estuaries. Most of the pathologies observed were parasites, and most

occurred in menhaden. High rates of gross pathological abnormalities and high densities of

macrophage aggregates may be associated with environmental contamination.

Coastal and Marine

Birds FL AL MS LA TX Gulf

Gulf of Mexico estuaries and wetlands provide essential habitat for migratory and resident

birds. Waterfowl use these ecosystems as winter feeding grounds. Resident wading birds

and marine birds rely on estuaries and wetlands for nesting and feeding. In general, gulf

estuaries and wetlands support large, healthy, stable populations of waterfowl and other

coastal birds.

Threatened Species FL AL MS LA TX Gulf

Many threatened and endangered species inhabit the gulf states but only four use estuaries

almost exclusively: brown pelican, Gulf sturgeon, manatee and Kemp’s ridley sea turtle. 

These species’ populations are stressed primarily because of degraded water quality and

habitat alterations. The brown pelican is stable in Florida and Alabama and, while population

numbers are low elsewhere, there is some evidence that they are increasing. There is little

information about the population stability of the Gulf sturgeon outside of Florida, and the

manatee is found routinely only in Florida. Manatee numbers are still low but appear to be

recovering slowly. The Kemp’s ridley sea turtle population has been steadily declining since

the 1940’s and is currently estimated to have only a thousand nesting females.
Ecological Report Card

50

Shellfish Bed Closures FL AL MS LA TX Gulf

Although the gulf region contains the most classified shellfish-growing waters in the U.S. 

(6.3 million acres in 1995), this region also has the most acreage of waters that are restricted

or prohibited for shellfish harvest. The percent of waters among the gulf states that were

harvest-restricted from 1985 to 1995 ranged from 24% to 43% with increases in restricted

waters over that time from 4% to 65%. Gulf waters lost 574,000 acres of approved shellfishgrowing waters between 1990 and 1995, mostly due to pollution from upstream sources and

wastewater treatment plants.

Tissue Contaminants FL AL MS LA TX Gulf

Environmental contaminants found in the edible tissue of fish and shellfish could potentially

pose a threat to human health. Seafood consumption advisories were issued in Florida,

Alabama, Louisiana, and Texas in 1997. EMAP-E analyzed 718 composite fish/shellfish

samples for chemical contaminants. Comparing the results to FDA and international

consumption guidelines yielded a low percentage of fish/shellfish with elevated

concentrations of contaminants.

Priority Ecological Indicators FL AL MS LA TX Gulf

Nutrients *

Dissolved oxygen *

Sediment contaminants *

Wetland *

Benthos *

Fish/shellfish landings

Fish biomarkers

Coastal and marine birds

Threatened species

Shellfish closures *

Fish tissue contaminants

* Key to color scheme where % area indicates the best estimate

of % area affected by adverse condition levels of the indicator.

Color % area Subjective rank

0-5% good; no problem

> 5-10% good-fair; minimal problem

>10-25% fair; moderate problem

>25-35% fair-poor; definite problem

>35% poor; severe problem
Ecological Report Card

51

The final product of this report is a report card that represents the best estimates of the extent

of ecological conditions based on the most recent available data. For the gulf estuaries

overall, most indicators ranked in fair condition. Minimal or no problems were observed for

fish and bird populations gulf-wide. Wetland loss and shellfish bed closures were rated as

definite or severe problems for almost all gulf states and these indicators presented the most

severe ecological concerns for gulf estuaries. Estuaries on the Florida gulf coast had

moderate problems identified by most of the indicators and, of all states, Florida rated most

similarly to the gulf overall. Alabama rated good to fair for most of the indicators, with

problems indicated by dissolved oxygen and fish biomarkers. Mississippi rated good to fair

for all indicators except wetland loss. Louisiana and Texas had definite problems with

nutrients. Fish tissue contaminants were a definite problem in Louisiana while degraded

benthic communities and fish health were indicated as problems in Texas.

The mix of colors in the report card suggest that estuaries in the Gulf of Mexico have some

significant environmental problems but that the extent of these problems varies among the

gulf states. There has been some improvement in the condition of estuaries since the Clean

Water Act was passed as indicated by the good condition of some estuarine fauna and the

relatively moderate problems with water quality and contaminants. The orange and red areas,

however, indicate that effective management and protection of estuaries must continue in the

Gulf of Mexico. Special attention should be directed toward stemming the loss of coastal

wetlands gulf-wide and improving the quality of wastewater and other effluents in order to

increase the acreage of shellfish beds that are approved for harvest.
52
53

Data Sources

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Interior, Fish and Wildlife Service, Washington, D.C.

Spendelow, J.A., and S.R. Patton. 1988. National Atlas of Coastal Waterbird Colonies in

the Contiguous United States: 1976-82. U.S. Department of the Interior, Fish and Wildlife

Service, National Wetlands Research Center. Biological Report 88(5). 326 p.

Saver, J.R., J.E. Hines, G. Gough, I. Thomas, and B.G. Peterjohn. 1997. The North

American Breeding Bird Survey Results and Analysis. Version 96.4. Pataxent Wildlife

Research Center, Laurel, MD.

www.mbr.nbs.gov:80/bbs/bbs.html

“Endangered Species Home Page” located at the web site for the U.S. Dept. of the Interior,

Fish and Wildlife Service

http://www.fws.gov/r9endspp/endspp.html

“Gulf Sturgeon” located at the web sites for U.S. Department of the Interior, Fish and

Wildlife Service and the National Marine Fisheries Service.

http://www.fws.gov/r4eao/gcsn1.html

http://kingfish.ssp.nmfs.gov/tmcintyr/fish/gulfstur.html

“Brown Pelican” located at the web sites for U.S. Department of the Interior, Fish and

Wildlife Service

http://www.fws.gov/r9endspp/i/b/sab2s.html

http://www.fws.gov/r9extaff/biologues/bio_plcn.html

Hawkins, D. 1997. Manatee Populations Rebound. In: People, Land, and Water. Volume 4. 

March 1997. U.S. Department of the Interior, Washington, D.C.

http://www.doi.gov/doi_plw.html

VanMeter, V.B. 1989. The West Indian Manatee in Florida. Florida Power & Light Co.,

Miami, FL. 41 p.

http://www.dep.state.fl.us/psm/webpages/booklet.html
Data Sources

63

O’Shea, T.J., B.B. Ackerman, and H.F. Percival. 1995. Population Biology of the Florida

Manatee. Information and Technology Report 1. U.S. Department of the Interior, National

Biological Service, Washington, D.C. 289 p.

“Kemp’s ridley sea turtle” located at the web sites for the Texas Parks and Wildlife

Department, the U.S. Fish and Wildlife Service, and the National Marine Fisheries Service.

http://www.tpwd.state./nature/endang/Kempsrid.htm

http://www.fws.gov/r9endspp/i/c/sac0r.html

http://kingfish.spp.nmfs.gov/tmcintyr/turtles/kemps.html

Hawkins, D. 1997. Manatee Populations Rebound. In: People, Land, and Water. Volume 4. 

March 1997. U.S. Department of the Interior, Washington, D.C.

http://www.doi.gov/doi_plw.html

Public Health

NOAA. 1991. The 1990 National Shellfish Register of Classified Estuarine Waters.

National Oceanic and Atmospheric Administration, National Ocean Service, Rockville, MD. 

100 p.

The 1995 National Shellfish Register of Classified Growing Waters” located at the web site

for the National Oceanic and Atmospheric Administration, National Ocean Service, Office of

Ocean Resources Conservation and Assessment.

http://www-orca.nos.noaa.gov/projects/95register/

“1997 Listing of Fish and Wildlife Advisories (LFWA) Database” located at the web site for

the U.S. Environmental Protection Agency, Office of Science and Technology.

http://www.epa.gov/OST/fishadvice/

“Commercial and Recreational Fisheries” located at the web site for NOAA, National Marine

Fisheries Service, Fisheries Statistics and Economics Division. 

http://remora.ssp.nmfs.gov/

U.S. EPA, EMAP-E Database for the Louisianian Province, 1991-1994. U.S. Environmental

Protection Agency, Gulf Ecology Division, Gulf Breeze, FL.

http://www.epa.gov/emap/

O’Connor, T.P. and B. Beliaeff. 1995. Recent Trends in Coastal Environmental Quality:

Results from the Mussel Watch Project 1986 to 1993. National Oceanic and Atmospheric

Administration, National Ocean Service, Silver Spring, MD. 46 p.
Data Sources

64

Lowe, J.A., D.R.G. Farrow, A.S. Pait, S.J. Arenstam and E.F. Lavan. 1991. Fish Kills in

Coastal Waters, 1980-1989. National Oceanic and Atmospheric Administration, National

Ocean Service, Office of Ocean Resources Conservation and Assessment, Rockville, MD. 

69 p.

“Animal and Plant Mortalities in the U.S.” located at the web site for the National Office for

Marine Biotoxins and harmful Algal Blooms, Woods Hole Oceanographic Institution, Woods

Hole, MA.

http://www.redtide.whoi.edu/hab/HABdistribution/ICESmap/USmortalities.gif

“The Gulf of Mexico Aquatic Mortality Response Network (GMNET)” located at the web

site for U.S. Environmental Protection Agency, Gulf of Mexico Program.

http://pelican.gmpo.gov/gmnet/gmhome.html
65

Appendix I: 

National Estuary Programs (NEP) and National Estuarine

Research Reserve Systems (NERRS) in the Gulf of Mexico

The Sarasota Bay NEP

The Sarasota Bay NEP began in 1989 in response to public concern

about pollution and habitat loss from rapid growth, development, and

overuse. Fifty years ago, Sarasota Bay was described as a pristine

estuary with lush seagrass meadows, abundant fish and shellfish, and

clean, clear water. Since then, Sarasota Bay has lost 40% of its

wetlands and suffers from high nutrient loading from nonpoint

sources and toxic contamination of sediments. Through the Sarasota

Bay NEP, a baywide monitoring program was instituted to evaluate

the status of and trends in priority problems such as nitrogen loadings and loss of wetland and

seagrass habitat. In order to improve management of the Bay’s resources, the program has

also recommended (1) an alternative development strategy which increases open space and

reduces stormwater runoff and (2) treated wastewater reclamation to be used as an alternative

water source. Sarasota Bay NEP homepage at

http://pelican.gmpo.gov/gulfofmex/estuarypartner/Sarasota/SarasotaBay.html

The Tampa Bay NEP

Recognizing the need for a comprehensive bay restoration and

protection plan, the Tampa Bay NEP was established in 1991 to

address the harmful effects of growth and development on the water

quality and wetland/seagrass habitats of Tampa Bay. The NEP has

sponsored research into the bay’s problems, tested early management

actions, and initiated several public outreach programs to get citizens

involved in protecting the bay. The NEP lists its priority concerns as

water and sediment quality, bay habitats, dredging and dredged

material management, fish and wildlife health, and spill prevention and response. Tampa

Bay has seen marked improvements in water quality and general health over the past several

years, and the goal of the NEP is to “. . . maintain this steady progress, even in the face of

continued growth.” Tampa Bay NEP homepage at http://access.tampabayrpc.org/nep
Appendix I

66

The Barataria-Terrebonne NEP

Many of the priority issues affecting the health

and stability of the Barataria-Terrebonne basin

relate back to hydrologic modifications,

including levees, dredge canals, and other

artificial structures that change the natural flow of water. In this basin, hydrologic

modifications have led to a reduction in the amount of sediment from the Mississippi River

that settles on the wetlands. The wetlands in this basin are subject to subsidence if the rate of

sediment building falls below the rate of sinking. Habitat loss affects the condition of living

resources and reduces the recreational and commercial value of wetlands and estuaries. 

Although habitat loss is the most pressing ecological issue facing the Barataria-Terrebonne

basin, the NEP is also concerned with eutrophication, pathogen contamination, and toxic

contamination. The NEP is currently developing a computer landscape model that will be

used to evaluate the impacts of actions that could be taken to conserve habitat in this

estuarine watershed. Barataria-Terrebonne NEP homepage at http:/www.btnep.org/

The Galveston Bay NEP

The Galveston Bay NEP was established in 1988 with a mission to

characterize, identify, and assess problems and issues affecting water

quality in Galveston Bay. The major problems affecting the bay are (1)

changes in the amount and timing of freshwater inflow that have

altered salinity patterns in the bay, (2) loss of wetland and seagrass

habitats, and (3) point and nonpoint sources of wastewater that

contribute toxic substances and bacterial contamination to water and

sediments and lead to poor water quality. The greatest challenge

facing the Galveston Bay NEP is finding a balance between competing

human uses and the environment. The NEP has designed a monitoring

program, has implemented management tools to enhance interagency coordination, and has

produced a “State of the Bay” report that characterizes the Galveston Bay ecosystem. 

Galveston Bay NEP homepage at http://gbep.tamug.tamu.edu/

The Corpus Christi Bay NEP

The Corpus Christi Bay NEP, established in 1992, is a community

based effort to identify the problems facing the bays and estuaries of

the Texas Coastal Bend. The mission of the NEP is (1) to enhance

cooperation among business, government, and the general public to

identify priority problems needing attention, (2) to encourage the use

of appropriate and feasible management actions that will ensure

sustainable utilization of resources in the future, (3) to coordinate

research, planning, management, and public outreach efforts, and (4) to ensure that “everyone

has a voice in managing the Coastal Bend’s bays and estuaries.” The NEP is currently
Appendix I

67

investigating several priority issues: altered freshwater inflow, declines in living resources,

loss of wetlands and other habitats, degradation of water quality, altered estuarine circulation,

selected public health issues, and debris. These investigations will identify the status and

trends of water quality and living resources. Corpus Christi Bay NEP homepage at

http://www.sci.tamucc.edu/ccbnep/

The Charlotte Harbor NEP

Charlotte Harbor was named to the National Estuary Program in

1995. The NEP was established to address priority problems in

Charlotte Harbor, including hydrologic alterations, water quality

degradation, and fish and wildlife habitat loss. As urban development

increases in the watershed, local governments are faced with

balancing conflicting needs for a reliable water supply, treating

residential wastewater, and preserving habitat. The goals of the Charlotte Harbor NEP are to

(1) improve environmental integrity; (2) preserve, restore, and enhance seagrass and

wetlands; (3) reduce point and nonpoint pollution; (4) provide proper freshwater inflow; and

(5) develop and implement a strategy for public participation and education as well as a

formal management plan to achieve these goals. Charlotte Harbor NEP homepage at

http://www.epa.gov/region4/waterpgs/water/coastal/chnep.htm

The Mobile Bay NEP

Mobile Bay was designated as a NEP in 1995. Mobile Bay NEP is

currently working towards prioritizing the environmental problems of

Mobile Bay by holding monthly workshops that involve the public and

the Technical and Citizens Advisory Committees. These workshops

allow everyone to voice their concerns about the bay and to come to

consensus on priority issues. Concurrently, a scientific literature

review will compile and analyze the existing data for Mobile Bay

water quality, living resources, and human uses. Mobile Bay NEP

homepage at http://www.epa.gov/OWOW/estuaries/mobile.htm

Weeks Bay NERRS

Weeks Bay is a small, shallow, estuarine embayment off Mobile Bay, fringed with marsh and

forested wetland. Designated an Outstanding National Water Resource in 1992, the Weeks

Bay watershed is ideally sized for estuarine research projects. Research from before 1990

focused primarily on obtaining baseline data, including projects on SAV type and abundance,

nursery habitats and indicator species since little was known about the relatively pristine and

unimpacted rural bay. Post-1990 research has included estuarine modeling, studies of salinity

regime, non-point source pollution and land-use studies, nutrient production and input,

community and habitat studies, migratory bird banding, and pesticide impacts. Current
Appendix I

68

research efforts at the Weeks Bay NERR and within its watershed include hydrodynamic

modeling, floral and faunal inventories and ongoing assessment and abatement of nonpoint

pollution. 

Apalachicola Bay NERRS

The Apalachicola Bay is the largest of the currently existing NERR sites, with 193,758 acres

of land and water within its boundaries, and potential for considerable expansion. The overall

high water quality of the Apalachicola estuary, combined with other factors, provides ideal

living conditions for estuarine biota, resulting in a highly productive estuarine system. The

myriad of habitats found within the reserve support a wide range of plant and animal species,

many of which are threatened or endangered. Research activities of the reserve include

long-term monitoring of physical, chemical, and biological parameters important to estuarine

productivity; a marsh restoration/breakwater demonstration program; on-site assistance for

regional research projects; and protection and monitoring programs for threatened sea turtles

and migratory bird nests. An onsite, computerized library consisting of over 3,700

publications is available for use by visiting researchers. From 1990 to 1995, over 40 research

and monitoring projects were undertaken by staff and outside investigators. 

Rookery Bay NERRS

The Rookery Bay NERR is located at the northern end of the Ten Thousand Islands on the

gulf coast of Florida, one of the largest mangrove-forested regions in the U.S. Rookery Bay

represents one of the few remaining undisturbed mangrove estuaries in North America.

Pristine mangrove forests surround shallow bay waters and the upland buffer consists of pine

flatwoods and dry-zone scrub. Visiting scientists utilize on-site laboratory facilities for

systems and baseline studies of the plant and animal communities of the reserve. Research

conducted at the site has included the study of nutrient cycling in mangrove systems,

estuarine food webs, estuarine faunal abundance, and bird population dynamics. Long-term

ecological monitoring efforts of the Rookery Bay NERR include water quality monitoring

(physical, chemical, and biological), meteorological and tidal conditions, and benthic

invertebrates. Data generated from the research programs are used to assess the health of the

Rookery Bay ecosystem, guide future research efforts, and develop new management policies

and educational programs for the reserve.
69

Appendix II: 

Characteristics of Estuaries in the Gulf of Mexico

Definitions

Low Water Clarity = < 10% Transmission of ambient light to 1 m depth

High TDN = Total dissolved nitrogen >= 1 mg/L

High Chlorophyll = Chlorophyll a > 20 ug/L

Hypoxia = at least 1 event of DO >0, <= 2 mg/L

Anoxia = at least 1 event of DO =0 mg/L

Low DO = Minimum bottom dissolved oxygen conc. over 12 hours is < 2 mg/L

High Sediment Contaminants = more than 5 analytes had concentrations > ER-L (Long et al. 1995)

Coastal Wetlands includes Salt/Fresh Marsh, Forested Scrub/Shrub, Tidal Flats

SAV = Submerged Aquatic Vegetation

Degraded Benthos = Benthic index < criteria for a province

% Fish with Pathology = Number of fish with observed pathology / number of fish sampled

Harvest Limited Shellfish Beds include beds conditionally approved, restricted, & prohibited for harvest
Appendix II

70

Estuary

Surface Area(sq. km)7

Total Drainage Area(100 sq km) 7

Avg. Depth (m) 2

Avg. Daily FreshwaterInflow (100 cfs) 7

Avg. Salinity (ppt) 2Avg. % Silt-Clay 2

% Area with Low Water Clarity 2% Area with High TDN 1% Area with High Chlorophyll 1

Florida Bay 1393 28 2 31 37 0 10 10

Ten Thousand Islands 697 62 3 17 42 50 27 0

Charlotte Harbor 805 130 2 48 13 9 67 42 22

Sarasota Bay 114 8 2 4 30 2 0 0 25

Tampa Bay 896 67 3 24 27 11 0 <1 43

St. Josephs Bay 170 2 10 66 40 0

Waccasassa Bay 40 44 1 26 22 0

Suwannee Sound 109 264 2 112 16 58 96 0 0

Apalachee Bay 412 119 3 53 30 17 16 0 0

Apalachicola Bay 554 531 3 291 22 32 12 7 0

St. Andrew Bay 243 28 4 45 31 7 0 0 0

Choctawhatchee Bay 334 140 5 85 25 61 <1 0 0

Pensacola Bay 370 181 4 116 23 43 <1 <1 <1

Perdido Bay 130 31 3 22 15 78 8 0 0

Mobile Bay 1059 1155 3 793 19 72 <1 0 0

Mississippi Sound 4792 697 4 436 24 60 5 <1 <1

Lake Borgne 730 383 3 251 7 75 9 n/a n/a

Lake Pontchartrain 1839 142 3 107 2 74 13 <1 0

Breton/Chandeleur Sounds 5403 65 3 103 27 46 9 0 n/a

Mississippi River 1554 29311 6 4644 6 77 36 100 0

Barataria Bay 1673 57 2 55 13 67 23 100 100

Terrebonne/Timbalier Bays 1761 41 2 46 18 62 3 0 100

Atchafalaya/Vermilion Bays 1821 2606 2 2238 1 83 59 100 70

Calcasieu Lake 256 111 1 63 12 63 99 25 100

Sabine Lake 243 541 2 172 11 48 6 0 0

Galveston Bay 1399 635 2 152 11 61 39 <1 0

Brazos River 5 5 3 74 28 96 0 0 0

Matagorda Bay 1093 1093 2 53 19 68 32 20 2

San Antonio Bay 531 531 2 41 13 71 72 44 20

Aransas Bay 539 539 3 10 15 87 0 0 1

Corpus Christi Bay 497 497 3 12 22 73 34 <1 4

Laguna Madre 1507 1507 2 9 36 32 0 1 75

Sources of Data: 1

 NOAA (1997) Estuarine Eutrophication Survey

2

 EMAP-E Louisianian Province (1991-1994) and West Indian Province (1995) database

3

 NOAA (1991) Coastal Wetlands of the United States

4

 Deegan et al. (1986) in Estuarine Variability

5

 NOAA (1995) National Shellfish Register
Appendix II

71

Estuary

% Area withHypoxia1

% Area with Anoxia1% Area with LowDO2% Area with HighSedimentContaminants2Coastal Wetlands (1000 acres)3SAV (1000 acres)4% Area with Degraded Benthos2% Fish withPathology2% Acres of HarvestLimited ShellfishBeds5

Florida Bay 100 15 3 3 260 12

Ten Thousand Islands 58 46 0 50 2165 5 50 7

Charlotte Harbor 48 42 0 11 624 53 89 50

Sarasota Bay 25 25 0 0 9 3 9 9 50 100

Tampa Bay 14 10 8 8 252 30 58 69

Waccasassa Bay 0 4 91 0 0

Suwannee Sound 0 0 0 32 229 8 4 0 52

Apalachee Bay 3 <1 0 0 695 32 0 0 100

Apalachicola Bay 14 0 36 26 592 9 5 0 71

St. Josephs Bay 100 0 100 0

St. Andrew Bay 13 13 0 0 251 13 0 0 100

Choctawhatchee Bay 54 23 55 42 280 3 58 3.25 100

Pensacola Bay 16 0 25 62 245 8 25 0 100

Perdido Bay 48 1 100 92 170 0 100 0 100 6

Mobile Bay 46 8 32 61 655 5 19 0.03 100

Mississippi Sound 19 <1 19 6 1069 30 18 <0.01 63

Lake Borgne 0 0 0 0 0 0.01 17 6

Lake Pontchartrain 25 9 9 22 8 0 13 0.01 100 6

Breton/Chandeleur Sounds 13 5 20 5 8 14 5 0.01 18

Mississippi River 0 0 58 8

 0 76 0.01 92

Barataria Bay 22 14 11 0 0 0.05 41

Terrebonne/Timbalier Bays 0 0 7 7 16 0.02 13

Atchafalaya/Vermilion Bays 5 3 <1 23 462 54 0.04 100

Calcasieu Lake 50 10 0 1 122 0 0 0 100

Sabine Lake 10 0 0 0 239 0 44 0.58 100

Galveston Bay 21 <1 <1 17 394 18 45 0.06 61

Brazos River 47 0 0 100 20 100 0.03 100

Matagorda Bay 25 0 1 2 86 7 22 0.09 23

San Antonio Bay 20 0 0 13 67 16 80 0.01 35

Aransas Bay 0 0 49 0 97 21 98 0 24

Corpus Christi Bay 23 0 0 15 30 13 21 0 26

Laguna Madre 17 7 0 0 451 191 24 0 79

Sources of Data: 6

 NOAA (1990) National Shellfish Register

7

 NOAA (1990) Estuaries of the United States

8

 National Biological Service (1995) Our Living Resources

9

 Personal Communication K. Gustafrom, Sarasota NEP

The Ecological Condition of Estuaries in the Gulf of Mexico is a joint

publication by U.S. EPA's Gulf Ecology Division and USGS/NWRC's Gulf

Breeze Project Office (EPA 620-R-98-004, July 1999). As another means of

distribution, we have created a CDROM product which provides 2

versions of the document in Adobe Systems Incorporated's portable

document format (PDF) - the first is a "low-resolution" version suitable for

viewing purposes; the second is a "high-resolution" version suitable for

high quality printing purposes.

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