Scientific Assessment of Hypoxia 

in U.S. Coastal 

Waters

Interagency Working Group 

on Harmful Algal Blooms, Hypoxia, and 

Human Health 

September 2010

Dissolved oxygen (mg/L)

Salinity

Depth (m)

0 6

32 34

0

80
This document should be cited as follows:

Committee on Environment and Natural Resources. 2010. Scientific Assessment of Hypoxia 

in U.S. Coastal Waters. Interagency Working Group on Harmful Algal Blooms, Hypoxia, and 

Human Health of the Joint Subcommittee on Ocean Science and Technology. Washington, 

DC. 

Acknowledgements:

Many scientists and managers from Federal and state agencies, universities, and research 

institutions contributed to the knowledge base upon which this assessment depends. Many 

thanks to all who contributed to this report, and special thanks to John Wickham and Lynn 

Dancy of NOAA National Centers for Coastal Ocean Science for their editing work. 

Cover and Sidebar Photos:

Background Cover and Sidebar: MODIS satellite image courtesy of the Ocean Biology 

Processing Group, NASA Goddard Space Flight Center. 

Cover inset photos from top: 1) CTD rosette, EPA Gulf Ecology Division; 2) CTD profile taken 

off the Washington coast, project funded by Bonneville Power Administration and NOAA 

Fisheries; Joseph Fisher, OSU, was chief scientist on the FV Frosti; data were processed 

and provided by Cheryl Morgan, OSU); 3) Dead fish, Christopher Deacutis, Rhode Island 

Department of Environmental Management; 4) Shrimp boat, EPA. 
Scientific Assessment of Hypoxia in U.S. Coastal Waters i
ii Scientific Assessment of Hypoxia in U.S. Coastal Waters

 This report is dedicated to the memory of Dr. Peter Eldridge, who was a 

member of the hypoxia report writing team and a research scientist with the U.S. 

Environmental Protection Agency. Peter had a great love and passion for the ocean, 

the environment, and science. Among Peter’s scientific contributions was the 

development of ecosystem models to address coastal environmental issues, such 

as coastal hypoxia, food web changes, and seagrass loss. Peter’s friendship and 

enthusiasm for science will be greatly missed.

Peter Eldridge (1946 – 2008)
Scientific Assessment of Hypoxia in U.S. Coastal Waters iii

Arctic Research Commission 

John Farrell

Department of Agriculture 

Louie Tupas 

Department of Commerce 

National Oceanic and Atmospheric 

Administration 

Craig McLean

Steve Murawski 

Roger Parsons 

Department of Defense 

U.S. Army Corps of Engineers 

Charles Chesnutt 

Joan Pope 

Department of Defense 

Office of Naval Research 

Linwood Vincent

James Eckman 

Department of Energy 

Office of Science 

Julie Carruthers 

James Ahlgrimm 

Department of Health and Human Services 

Centers for Disease Control and Prevention 

Lorraine Backer 

G. David Williamson 

Department of Health and Human Services 

Food and Drug Administration 

Robert Dickey

William Jones 

Department of Health and Human Services 

National Institutes of Health 

Allen Dearry 

Department of Homeland Security 

U.S. Coast Guard 

Jonathan Berkson 

Department of the Interior

Kameran Onley

Tim Petty

Department of the Interior 

Minerals Management Service 

James Kendall 

Walter Johnson

Department of the Interior 

United States Geological Survey 

John Haines

Linda Gunderson

Department of Justice 

Matt Leopold

Amber Blaha 

Department of State 

David Balton 

Liz Tirpak 

Department of Transportation 

Maritime Administration 

Richard Corley

U.S. Environmental Protection Agency 

Kevin Teichman

Steven Hedtke 

Executive Office of the President 

Council on Environmental Quality 

Hardy Pearce

Executive Office of the President 

Domestic Policy Council 

Paul Skoczylas

Executive Office of the President 

Office of Management and Budget 

Stuart Levenbach

Kimberly Miller

Executive Office of the President 

Office of Science and Technology Policy 

Jerry Miller

Joint Chiefs of Staff 

Robert Winokur 

Nadeem Ahmad

National Aeronautics and Space 

Administration 

Jack Kaye 

Eric Lindstrom 

National Science Foundation 

Tim Killeen

Julie Morris 

Phil Taylor

Marine Mammal Commission 

Robert Gisiner

Tim Ragen

Smithsonian Institution 

Leonard Hirsch 

Joint Subcommittee on Ocean Science and Technology 

(JSOST)

Steve Murawski, DOC/NOAA, Co-Chair

Tim Killeen, NSF, Co-Chair

Jerry Miller, OSTP, Co-Chair
iv Scientific Assessment of Hypoxia in U.S. Coastal Waters

Lorraine C. Backer (Co-Chair)

Centers for Disease Control and Prevention

Paul A. Sandifer (Co-Chair)

National Oceanic and Atmospheric Administration

Paula Bontempi

Alternate: Fredric Lipschultz

National Aeronautics and Space Administration

Herbert T. Buxton

United States Geological Survey

David Garrison

National Science Foundation

Rob Magnien

Alternate: Quay Dortch

National Oceanic and Atmospheric Administration

Steven Plakas

U.S. Food and Drug Administration 

Tim Ragen

Alternate: Bob Gisiner

Marine Mammal Commission

Teri Rowles

National Oceanic and Atmospheric Administration

Joyce Saltsman

U.S. Food and Drug Administration 

Juli Trtanj

National Oceanic and Atmospheric Administration

Frederick L. Tyson

National Institute of Environmental Health 

Sciences

Usha Varanasi

Alternate: Walton Dickhoff

National Oceanic and Atmospheric Administration

William Russo

U.S. Environmental Protection Agency

Mark Walbridge

Department of Agriculture

Scientific support staff:

Elizabeth B. Jewett

Cary B. Lopez

Carolyn Sotka

Virginia Fay

National Oceanic and Atmospheric Administration

Cheryl L. Fossani

National Science Foundation

JSOST Interagency Working Group on 

Harmful Algal Blooms, Hypoxia and Human Health (IWG-4H)

Primary Authors 

Elizabeth B. Jewett, Cary B. Lopez, David M. 

Kidwell, Suzanne B. Bricker

National Oceanic and Atmospheric Administration

Marianne K. Burke , Mark R. Walbridge

U.S. Department of Agriculture

Peter M. Eldridge , Richard M. Greene, James 

D. Hagy III 

U.S. Environmental Protection Agency

Herbert T. Buxton

U.S. Geological Survey 

Robert J. Diaz

Virginia Institute of Marine Science

Major Contributors

Cheryl Brown

U.S. Environmental Protection Agency

Bill Peterson

National Oceanic and Atmospheric Administration

Jay Peterson and Cheryl Morgan

Oregon State University
Scientific Assessment of Hypoxia in U.S. Coastal Waters v

Table of Contents

vi List of Figures

vi List of Tables

vii List of Boxes

vii List of Case Studies

viii List of Acronyms

1 Executive Summary

7 Chapter 1. Legislative Background, Report Overview and Development 

Process

11 Chapter 2. Causes and Status of Hypoxia in U.S. Coastal Waters

25 Chapter 3. Federal Hypoxia and Watershed Science Research: Status and 

Accomplishments

47 Chapter 4. Future Research Directions and Interagency Coordination

57 References

68 Appendices

69 Appendix I. Federal Agency Hypoxia or Hypoxia-related Research

83 Appendix II. Geographic Case Studies

118 Appendix III. Table of U.S. Systems Impacted by Hypoxia
vi Scientific Assessment of Hypoxia in U.S. Coastal Waters

Page #

12 Figure 1. Global distribution of systems affected by low dissolved oxygen.

14 Figure 2. Change in number of U.S. coastal areas experiencing hypoxia from 12 documented areas in 1960 

to over 300 now.

15 Figure 3. Comparison of the relative contribution of major sources of nitrogen pollution in three coastal 

ecosystems experiencing hypoxia.

16	 Figure 4. Conceptual diagram illustrating development and effects of hypoxia in stratified waters.

18 Figure 5. The range of ecological impacts exhibited as dissolved oxygen levels drop from saturation to 

anoxia. 

19	 Figure 6. Conceptual view of how hypoxia alters ecosystem energy flow with example systems.

23 Figure 7. Relative magnitude and contribution of land management practices versus climate change factors 

to expansion or contraction of low dissolved oxygen.

25	 Figure 8. Conceptual diagram explaining how, in an adaptive management framework, scientific research

informs management of environmental problems such as hypoxia.

27 Figure 9. Schematic describing general areas of hypoxia-related research.

29 Figure 10. Hypoxia is most intensively monitored in the largest and most impacted coastal systems in the 

United States. Examples include: a) Long Island Sound, b) Chesapeake Bay, c) Lake Erie, and d) Northern 

Gulf of Mexico.

31 Figure 11. Ensemble forecasts of the response of hypoxia to changes in riverine nitrogen load.

33 Figure 12. Trends in catch per unit effort for brown shrimp in the northern Gulf of Mexico.

34 Figure 13. Relationship between annual landings of brown shrimp in the northern Gulf of Mexico and the 

size of the hypoxic zone.

35	 Figure 14. Map of Gulf of Mexico with darker shaded areas indicating denser fish populations in the1960s.

37 Figure 15. Estimated nitrate delivery to the Gulf of Mexico for April, May, and June in1979 - 2008.

40	 Figure 16. Percent of the United States drained by artificial means such as tile drains.

42 Figure 17. 2007 Map of CEAP projects.

83 Figure A1. Geographic locations of hypoxia case studies.

List of Figures

List of Tables

Page #

13 Table 1. Percentage of U.S. estuaries and coastal water bodies with reports of hypoxia.

20 Table 2. Principal ecosystem characteristics and services impacted by hypoxia.

21 Table 3. Examples of hypoxia-related economic impacts.

22	 Table 4. Estimated influence of climate drivers on the extent and severity of hypoxia.

30 Table 5. Models developed since 2002 to forecast or simulate Gulf of Mexico hypoxia.

84 Table A1. Comparison of Physical Systems Represented by Case Studies in Appendix II.
Scientific Assessment of Hypoxia in U.S. Coastal Waters vii

Page #

7 Box 1. HABHRCA 2004 Reports and Assessments

8 Box 2. Legislation Relevant to Hypoxia

11	 Box 3. Hypoxia Definition

26 Box 4. Adaptive Management Approach for Gulf of Mexico Hypoxic Zone

27 Box 5. Adaptive Management Approach for Chesapeake Bay

28	 Box 6. Sound Science Leads to Significant Reductions in Hypoxia in Long Island Sound

29 Box 7. Hypoxia Advanced Warning Protects Drinking Water

38 Box 8. Application of SPARROW for Reducing Nutrients to the Gulf of Mexico

39 Box 9. EPA Works Closely With States to Develop and Adopt Nutrient Criteria

41 Box 10. Soil Drainage Research in Ohio

43 Box 11. Monitoring Winter Cover Crop Performance from Space

43	 Box 12. USDA Conservation Research Program Benefits in the Mississippi River Basin

54 Box 13. USGS Deployment of New Instruments to Measure Water Flow and Sediment Flux

List of Boxes

Page #

85 Long Island Sound

89 Lake Erie

92 Chesapeake Bay

99 Pensacola Bay

102 Northern Gulf of Mexico

108	 Northeast Pacific Continental Shelf

112 Yaquina Bay

116 Hood Canal

List of Case Studies
viii Scientific Assessment of Hypoxia in U.S. Coastal Waters

ADMS Agricultural Drainage Management Systems

ARS Agricultural Research Service, USDA

BMP best management practice

CBEMP Chesapeake Bay Environmental Model 

Package 

CEAP Conservation Effects Assessment Project

CENR Committee on Environment and Natural 

Resources

CHRP Coastal Hypoxia Research Program, NOAA

CRP Conservation Reserve Program, USDA

CSREES Cooperative State Research, Education, and 

Extension Service, USDA

DOD U.S. Department of Defense

DOE U.S. Department of Energy

DOI U.S. Department of the Interior

EISA Energy Independence and Security Act of 2007

EMAP Environmental Monitoring and Assessment 

Program

EMVL Environmental Modeling and Visualization 

Laboratory

EPA U.S. Environmental Protection Agency

ERS Economic Research Service, USDA

FSA Farm Service Agency, USDA

FVCOM Finite Volume Community Ocean Model

GLNPO Great Lakes National Program Office, EPA

HAB harmful algal bloom

HABHRCA Harmful Algal Bloom and Hypoxia Research 

and Control Act

HCDOP Hood Canal Dissolved Oxygen Program

IFYLE International Field Years on Lake Erie

IOOS Integrated Ocean Observing System

IWG-4H Interagency Working Group on HABs, Hypoxia, 

and Human Health

LaMP Lakewide Management Plan, Lake Erie

LISS Long Island Sound Study

LMAV Lower Mississippi Alluvial Valley

LUMCON Louisiana Universities Marine Consortium

MARB Mississippi Atchafalaya River Basin 

MDA Maryland Department of Agriculture

NASA National Aeronautics and Space Administration

NAWQA National Water-Quality Assessment Program, 

USGS

NBEP Narragansett Bay Estuary Program 

NCER National Center for Environmental Research, 

EPA

NCII Nutrient Control Implementation Initiative 

NEP National Estuary Program, EPA

NERL National Exposure Research Laboratory, EPA

NERRS National Estuarine Research Reserve System, 

NOAA 

NHEERL National Health and Environment Effects 

Research Laboratory, EPA

NMFS National Marine Fisheries Service, NOAA

NOAA National Oceanic and Atmospheric 

Administration, U.S. Department of Commerce

NRC National Research Council

NRCS Natural Resources Conservation Service, USDA

NRL Naval Research Laboratory, U.S. Department of 

Defense

NRMRL National Risk Management Research 

Laboratory, EPA

NSF National Science Foundation

OST Office of Science and Technology, EPA

OW Office of Water, EPA

OWOW Office of Wetlands, Oceans, and Watersheds,

EPA

PDO model Nitrogen-Phytoplankton-Detritus-Oxygen 

model

ReCON Real-time Coastal Observation Network

REMM Riparian Ecosystem Management Model

ReNuMa Regional Nutrient Management Model

ROMS Regional Ocean Model System

RZWQM Root Zone Water Quality Model 

SAV submerged aquatic vegetation

SEAMAP Southeast Area Monitoring and Assessment 

Program, NOAA

SPARROW SPAtially Referenced Regressions On 

Watershed Attributes

STAR Science to Achieve Results Program, EPA

STEWARDS Sustaining the Earth’s Watersheds 

Through Research, Data Analysis, and Synthesis 

STORET STOrage and RETrieval data system, EPA

SWAT Soil and Water Assessment Tool

SWMP System-Wide Monitoring Program

SWWRP System-Wide Water Resources Program

TMDL total maximum daily load

USACE U.S. Army Corps of Engineers, DOD

USDA U.S. Department of Agriculture

USFWS U.S. Fish and Wildlife Service, DOI

USGS U.S. Geological Survey, DOI

WRSIS Wetland Reservoir Subirrigation System

List of Acronyms
Scientific Assessment of Hypoxia in U.S. Coastal Waters 1

The Problem

The occurrence of hypoxia, or low dissolved oxygen, is increasing in coastal waters 

worldwide and represents a significant threat to 

the health and economy of our Nation’s coasts 

and Great Lakes. This trend is exemplified 

most dramatically off the coast of Louisiana and 

Texas, where the second largest eutrophicationrelated hypoxic zone in the world is associated 

with the nutrient pollutant load discharged by the 

Mississippi and Atchafalaya Rivers. 

Aquatic organisms require adequate dissolved 

oxygen to survive. The term “dead zone” is often 

used in reference to the absence of life (other 

than bacteria) from habitats that are devoid of 

oxygen. The inability to escape low oxygen areas 

makes immobile species, such as oysters and 

mussels, particularly vulnerable to hypoxia. These 

organisms can become stressed and may die due to 

hypoxia, resulting in significant impacts on marine 

food webs and the economy. Mobile organisms 

can flee the affected area when dissolved oxygen 

becomes too low. Nevertheless, fish kills can result 

from hypoxia, especially when the concentration 

of dissolved oxygen drops rapidly. New research 

is clarifying when hypoxia will cause fish kills as 

opposed to triggering avoidance behavior by fish. 

Further, new studies are better illustrating how 

habitat loss associated with hypoxia avoidance 

can impose ecological and economic costs, such 

as reduced growth in commercially harvested 

species and loss of biodiversity, habitat, and 

biomass. Transient or “diel-cycling” hypoxia, 

where conditions cycle from supersaturation of 

oxygen late in the afternoon to hypoxia or anoxia 

near dawn, most often occurs in shallow, eutrophic 

systems (e.g., nursery ground habitats) and may 

have pervasive impacts on living resources because 

of both its location and frequency of occurrence. 

Although coastal hypoxia can be caused by 

natural processes, a dramatic increase in the 

number of U.S. waters developing hypoxia is 

linked to eutrophication due to nutrient (nitrogen 

and phosphorus) and organic matter enrichment 

resulting from human activities. Sources of 

enrichment include point source discharges 

of wastewaters, nonpoint source atmospheric 

deposition, and nonpoint source runoff from 

croplands, lands used for animal agriculture, 

and urban and suburban areas. The incidence of 

hypoxia has increased ten-fold globally in the past 

50 years and almost thirty-fold in the United States 

since 1960, with more than 300 systems recently 

experiencing hypoxia (Diaz & Rosenberg 2008; 

Table 1 and Appendix III).

Diffuse runoff from nonpoint sources, such 

as agriculture fields, can be difficult to control, 

although improved production methods that 

reduce tillage, optimize fertilizer application, 

and buffer fields from waterways can mitigate 

water quality impairments. Despite the use of 

improved production methods in recent years, 

agriculture is still a leading source of nutrient 

pollution in many watersheds due, in part, to 

the high demand for nitrogen-intensive crops, 

principally corn. Furthermore, drainage practices, 

including tile drainage, have brought wetlands into 

crop production, short-circuited pathways (such 

as denitrification) that could ameliorate nutrient 

loading, and increased the transport of nitrogen 

into waterways. Atmospheric nitrogen deposition 

due to fossil fuel combustion has declined in many 

areas due to emission controls, but it remains an 

important source of diffuse nutrient loading. The 

difficulty of reducing nutrient inputs to coastal 

waters results from the close association between 

nutrient loading and a broad array of human 

activities in watersheds and explains the growth in 

the number and size of hypoxic zones.

Unfortunately, hypoxia is not the only stressor 

impacting coastal ecosystems. Overfishing, 

harmful algal blooms (HABs), toxic contaminants, 

and physical alteration of coastal habitats 

associated with coastal development are several 

problems that co-occur with hypoxia and interact 

to decrease the ecological health of coastal waters 

and reduce the ecological services that they can 

provide. 

Executive 

Summary
2 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Executive Summary

Legislative Mandates for 

Action

The Harmful Algal Bloom and Hypoxia 

Research and Control Act (HABHRCA) mandated 

creation of this report, which serves as a thorough 

update to the first scientific assessment of hypoxia 

released in 2003. Several other legislative 

drivers also influence how Federal agencies 

work on coastal water quality including the 

Clean Water Act; the Food, Conservation, and 

Energy Act of 2008 (“Farm Bill”); the Energy 

Independence and Security Act of 2007; and the 

Coastal Zone Management Act. Responsibility 

for resolving hypoxia spans several Federal 

agencies (U.S. Department of Agriculture, U.S. 

Geological Survey, U.S. Environmental Protection 

Agency, and National Oceanic and Atmospheric 

Administration), which oversee research and 

management/control programs (Appendix I). 

States play a critical role in monitoring and 

managing hypoxia, but their efforts are not 

addressed in detail here because this report was 

mandated to focus on Federal efforts.

Adaptive Management

Adaptive management recognizes that science 

should inform management decision-making, 

not only as the original questions are posed 

but as scientific understanding continues to 

develop. Current scientific understanding of the 

factors contributing to hypoxia is derived from 

rigorous research that Federal agencies have been 

conducting and funding for at least 25 years. 

Federal hypoxia research has made significant 

progress in describing and quantifying the causes 

of hypoxia and reducing uncertainties required to 

confidently proceed with an adaptive management 

approach. For example, the ecological mechanisms 

linking nutrient loading to hypoxia in the 

Chesapeake Bay were quantified sufficiently to 

justify an initial 40% nutrient reduction goal in the 

mid-1980s; further research and sophistication in 

simulation models have been used subsequently 

to support three additional rounds of adaptive 

management leading to more detailed nutrient 

reduction strategies. 

From a national perspective, adaptive 

management approaches will have to be flexible 

enough to address differences among ecosystems 

(e.g., geography, level of watershed development, 

agricultural influence, nutrient loading, physical 

circulation of the waterbody) and future 

contingencies as they unfold. For example, 

it is likely that climate change will affect the 

incidence of hypoxia in coastal waters. A flexible 

management approach will enable response to 

climate impacts as they are realized. A flexible 

and meaningful adaptive management strategy 

for agricultural production―including biofuels―

should be explored in order to ensure that 

agricultural products are produced in a manner that 

minimizes or prevents water quality impairments. 

Reducing hypoxia via nutrient loading 

reductions will require a concerted effort by a 

diverse group of stakeholders. Implementing these 

actions will likely require organized programs to 

monitor, study, and manage water quality problems. 

Such programs have already been established for 

a few coastal waterbodies (e.g., Lake Erie, Gulf of 

Mexico, Chesapeake Bay, Long Island Sound). In 

the case of other waterbodies where the problem 

has just recently been recognized and understood 

(e.g., Narragansett Bay, Rhode Island; Pensacola 

Bay, Florida), only nascent efforts, if any, are in 

place to address it.

Scientists use the box corer to sample sediments with 

negligible disturbance. Sediment cores are used to study 

sediment-oxygen-nutrient dynamics.

Photo. L.Jewett, NOAA
Scientific Assessment of Hypoxia in U.S. Coastal Waters 3

Executive Summary

Federal Research 

Accomplishments 

and Opportunities for 

Advancement

Understanding and managing hypoxia requires 

research and management actions to address 

entire watersheds and their coastal receiving 

waters. This report examines progress in: 1) 

understanding the dynamics of hypoxia where it 

occurs (i.e., in estuaries, coastal waters, and the 

Great Lakes); 2) understanding and monitoring 

nutrient fluxes in watersheds; and 3) understanding 

how to reduce nutrient transport across the 

landscape. Because responsibility for management 

of nutrient enrichment in watersheds is shared 

across several Federal agencies, coordination 

and information-sharing are critical. Presently, 

interagency collaboration is most extensive and 

effective in places where investments in scientific 

and management activities have been largest and 

sustained for the longest period of time (e.g., 

Chesapeake Bay). 

Responsibility for monitoring dissolved oxygen

in most coastal and Great Lakes waterbodies lies 

with states or with Federal-state partnerships that 

utilize state monitoring programs to track water 

quality. For many coastal and Great Lakes waters 

where hypoxia occurs, fairly rigorous methods 

have been implemented for measuring dissolved 

oxygen and conveying this information to scientists 

and the public. However, the two largest hypoxic 

zones in the United States, located at the mouth 

of the Mississippi River and on the Oregon 

continental shelf, occur beyond the limits of state 

waters and, thus, rely on Federal support for 

monitoring. Monitoring informs coastal managers 

about water quality conditions in the ecosystems 

they oversee, and it helps support the development 

and verification of ecosystem simulation models 

used to guide management decisions.

Since the last scientific assessment of hypoxia 

was written in 2003, many computer models have 

been developed or updated to simulate ecological 

processes related to hypoxia in estuarine, 

coastal, and Great Lakes ecosystems and their 

watersheds. Sophisticated physical transport 

models, which examine ocean currents and mixing, 

are increasingly being coupled with water quality 

models to examine alternatives for managing 

hypoxia. These models are most effective when 

they reflect a strong scientific understanding of 

the processes that control hypoxia development. 

Relatively simple regression models can also be 

effective for testing hypotheses regarding factors 

that control hypoxia, especially as more longterm data on hypoxia become available. The 

relative simplicity of regression analyses has also 

made them useful tools for short-term ecological 

forecasting. Regression analyses have been used 

for annual hypoxia forecasts for the northern Gulf 

of Mexico and Chesapeake Bay. Ecological box 

models, which simplify processes into broader 

geographic resolution, have improved greatly 

and have begun to incorporate bioeconomic 

components for assessing impacts of hypoxia on 

commercial and recreational fisheries. Advances 

have been particularly dramatic in watershed 

science. Watershed models now allow scientists to 

quantify the contribution of particular geographic 

regions to nutrients entering a coastal system. A 

suite of models connecting sources of nutrients 

in watersheds to the development of hypoxia 

in receiving waters, ideally with quantified 

uncertainty, is needed by resource managers to 

Researchers retrieve the CTD rosette, used for collecting 

water and measuring dissolved oxygen and other 

oceanographic parameters, after a sampling profile is 

completed during rough seas. 

Photo: L.Jewett, NOAA
4 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Executive Summary

justify potentially costly actions to reduce nutrients 

and hypoxia. Use of a multiple model consensus, 

where models use different approaches and 

assumptions, provides one way to better inform 

management decisions. This approach is well 

known for its application to forecasting hurricane 

paths and predicting the effects of carbon dioxide 

fluctuations on climate.

Monitoring stream and river flow and the 

associated nutrients is critically important for 

evaluating nutrient sources in the watershed and 

modeling fluxes to coastal waterbodies. Stream 

and river monitoring was made more efficient, 

maximizing the use of existing resources, 

through the redesign of the National Stream 

Quality Accounting Network in 2007. However, 

it is important not only to maintain the current 

streamflow gauges and water quality monitoring 

stations, but also to increase the number of streams 

monitored. Similar to hypoxia monitoring, the 

monitoring of nutrients in rivers and streams is 

required for the development and use of predictive 

models and to determine the cause-effect 

relationships between activities that alter water 

nutrient export and the changes in water quality in 

the receiving water. Expanded stream monitoring, 

in combination with modeling efforts, will allow 

design of effective nutrient reduction strategies 

and will improve the ability to track progress 

toward water quality goals. Thus, effective and 

sustained management of hypoxia will require 

long-term support of stream and river water quality 

monitoring programs.

Research exploring hypoxia impacts on fish 

and invertebrates has shown negative effects on 

growth, reproduction, species composition, and 

ecological interactions among species. However, 

scaling up these impacts from individuals to entire 

fisheries populations or ecosystems is extremely 

complex and requires sophisticated ecosystem 

models that are generally beyond the state-ofthe-science. Thus, research should be focused 

on developing these models and linking them to 

those that include more conventional water quality 

components. An additional modeling challenge 

will be resolving the impacts of hypoxia on 

living resources in systems affected by a suite of 

stressors as we move toward more comprehensive 

ecosystem management approaches. 

Reducing nutrients from anthropogenic sources 

can lead to a reduction in coastal hypoxia and 

improvements in water quality throughout the 

watershed. Nutrient loads in some systems, such 

as Long Island Sound and Narragansett Bay, are 

being successfully reduced through targeting of 

wastewater treatment plants. However, nutrient 

loads from municipal and industrial facilities, 

defined as point sources, are more easily addressed 

than the diffuse sources of nutrients entering 

waterways as runoff from agricultural and urban 

lands. 

Significant Federal investments and scientific 

effort have focused on developing efficient and 

effective ways to reduce nutrient runoff, including 

land conservation programs (which provide 

incentives for farmers to take marginal agricultural 

land out of production, invest in working lands 

to reduce erosion and control nutrients, and reestablish wetlands), alternative drainage systems, 

remote sensing to target fertilizer applications, 

winter cover crops, and newly formulated 

fertilizers. 

Unfortunately, measures implemented on 

nonpoint sources to date have proven ineffective 

at reducing nutrient loads from large watersheds 

to levels needed to significantly reduce hypoxic 

zones. For example, reductions in total spring 

nitrogen loads to the Gulf of Mexico from 2001-

2005 were primarily from forms of nitrogen 

other than nitrate, which is a critical form fueling 

spring primary production leading to hypoxia. 

This highlights the importance of the nutrient 

composition, as well as seasonality, for reduction 

targets. Further, evidence suggests that some 

ecosystems may not respond as expected to nutrient 

management as they become nutrient saturated. 

Thus, major new initiatives should include rigorous 

scientific evaluation of the effectiveness of existing 

nutrient reduction strategies through local analyses 

of downstream water quality so that strategies 

can be refined accordingly. Continued research 

is also needed on new practices, such as those 

that enhance natural nutrient processes through 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 5

Executive Summary

reforestation, river diversions into wetlands, and 

vegetation buffer systems for streams and rivers. 

Such research has already led to management 

decisions to protect wetlands and to reforest 

portions of watersheds. 

Establishment of criteria for acceptable nutrient 

levels in both coastal areas and in rivers upstream 

from hypoxic zones is also a critical tool for 

designing management plans. These criteria can 

also be used to measure progress. 

Conclusion

Hypoxia is a major contributor to the decline of 

coastal water quality observed in recent decades, 

and its extent has been expanding. It is part of the 

broader issue of nutrient-driven eutrophication. 

Eutrophication is also linked to increased HABs, 

loss of seagrasses, and other impacts on coastal 

ecosystems. For eutrophic ecosystems, concerted 

and coupled research and management efforts, 

along with stakeholder support, will be needed 

to rigorously identify, quantify, and implement 

nutrient reduction strategies that are effective and 

achievable. Furthermore, for systems such as the 

Oregon shelf where hypoxia is driven primarily by 

natural processes linked to variations in climate, 

improved scientific understanding will provide 

insight into future impacts of climate change on 

similar ecosystems. Moreover, knowledge gained 

will be important for developing forecasts of 

the extent and severity of low dissolved oxygen, 

which will help managers mitigate the impacts of 

hypoxia. 

If properly planned and executed, adaptive 

management of nutrient inputs will lead to 

significant reductions in hypoxia. However, if 

current practices are continued, the expansion 

of hypoxia in coastal waters will continue and 

increase in severity, leading to further impacts on 

marine habitats, living resources, economies, and 

coastal communities. 

Sunset aboard EPA’s Ocean Survey Vessel Peter W. Anderson during a research cruise in the Gulf of Mexico hypoxic zone.

Photo: EPA

Scientific Assessment of Hypoxia in U.S. Coastal Waters 7

Legislative 

Background, Report Overview, 

and Development Process

Chapter 1

1.1. Legislative Background 

In the early 1980s, concern about low dissolved 

oxygen in coastal waterbodies of the United States 

led to the first national assessment of coastal 

hypoxia (Whitledge 1985), which found dissolved 

oxygen levels in many U.S. waterbodies on the 

decline as a result of eutrophication. By the 1990s, 

serious and large-scale water quality problems were 

identified, including harmful algal blooms (HABs) 

and hypoxia, most prominently in the northern Gulf 

of Mexico, Lake Erie, Chesapeake Bay, and Long 

Island Sound. These problems led to a national 

assessment of eutrophication in 1999 (Bricker et al. 

1999), which was subsequently updated (Bricker et 

al. 2007), and an integrated assessment of hypoxia 

in the northern Gulf of Mexico (CENR 2000, U.S. 

EPA 2007), as well as the passage of the Harmful 

Algal Bloom and Hypoxia Research and Control 

Act of 1998 (HABHRCA, Public Law 105-383). 

HABHRCA was reauthorized by the Harmful 

Algal Bloom and Hypoxia Amendments Act of 

2004 (HABHRCA 2004, Public Law 108-456). 

HABHRCA 2004 reconstituted the Interagency 

Task Force on HABs and Hypoxia. To fulfill 

the requirements of both HABHRCA 2004 and 

the Oceans and Human Health Act of 2004, the 

Interagency Task Force on HABs and Hypoxia was 

incorporated into the Interagency Working Group 

on HABs, Hypoxia, and Human Health (IWG4H, see page iii) of the Joint Subcommittee on 

Ocean Science and Technology. HABHRCA 2004 

required five reports to assess and recommend 

research programs on HABs and hypoxia in 

U.S. waters, including this report, a Scientific 

Assessment of Hypoxia in U.S. Coastal Waters 

(Box 1). HABHRCA 2004 stipulates that this 

report should: 

• examine the causes, ecological consequences, 

and economic costs of hypoxia; 

• describe the potential ecological and economic 

costs and benefits of possible actions for 

preventing, controlling, and mitigating hypoxia; 

• evaluate progress made by and needs of Federal 

research programs; and 

• identify ways to improve coordination among 

Federal agencies with respect to research on 

hypoxia. 

HABHRCA 2004 also authorizes appropriations 

to the Secretary of Commerce and the National 

Oceanic and Atmospheric Administration (NOAA) 

to conduct research on hypoxia. 

Additional legislation affecting Federal 

research on hypoxia or factors that may affect 

hypoxia is listed in Box 2. The Coastal Zone 

Act Reauthorization Amendments of 1990 

reauthorized the Coastal Zone Management Act 

Box 1. HABHRCA 2004 Reports and 

Assessments

• Harmful Algal Bloom Management and 

Response: Assessment and Plan 

• National Assessment of Efforts to Predict and 

Respond to Harmful Algal Blooms in U.S. Waters 

(Prediction and Response Report) 

• Report on National Scientific Research, 

Development, Demonstration, and Technology 

Transfer Plan for reducing HAB Impacts (RDDTT 

Plan) 

• Scientific Assessment of Freshwater Harmful 

Algal Blooms 

• Scientific Assessment of Marine Harmful Algal 

Blooms 

• Scientific Assessment of Hypoxia in U.S. 

Coastal Waters
8 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 1

and established a joint program between the U.S. 

Environmental Protection Agency (EPA) and the 

states to develop and implement coastal nonpoint 

pollution management programs. We note that 

EPA’s Mississippi River Basin program will be 

enhanced in 2011, pending enactment of the 

President’s proposed budget. The Water Resources 

Development Act authorizes flood control, 

navigation, and environmental projects and studies 

by the U.S. Army Corps of Engineers (USACE), 

and it states that the Secretary of the Army may 

participate in assessments of hypoxia in the 

northern Gulf of Mexico. Some of this legislation 

focuses on water quality in upland watersheds, 

which ultimately may affect the quality of water 

delivered to coastal ecosystems; therefore, it also 

impacts coastal hypoxia. The Clean Water Act 

aims to restore and maintain the chemical, physical, 

and biological integrity of the Nation’s waters by 

reducing point and nonpoint pollution sources, 

providing assistance to publicly owned treatment 

works for improving wastewater treatment, 

and maintaining the integrity of wetlands. The 

Food, Conservation, and Energy Act of 2008 (the 

“Farm Bill”) authorized $25 billion to support 

conservation programs administered by the U.S. 

Department of Agriculture (USDA) through its 

Natural Resources Conservation Service (NRCS) 

and Farm Service Agency (FSA). Finally, the 

Energy Independence and Security Act (EISA) of 

2007 potentially has far-reaching environmental 

implications. The bill mandates production of 

36 billion gallons of biofuels by the year 2022, 

including 15 billion gallons of corn-based ethanol. 

The legislation designates the EPA, USDA, 

and U.S. Department of Energy (DOE) as lead 

agencies in an interagency effort to develop criteria 

for sustainable development of biofuels, which 

include prevention of water quality and ecosystem 

impairments.

1.2. Report Overview

This assessment focuses on the science that 

forms the basis for improving knowledge of the 

causes, impacts, and solutions for hypoxia in 

coastal ecosystems of the United States as of 2009. 

This report has four chapters and three appendices: 

• Chapter 1: Legislative background, report 

overview, and report development process;

• Chapter 2:The current status of hypoxia in U.S. 

coastal waters, the spectrum of causal factors 

contributing to hypoxia, and the ecological and 

economic consequences of hypoxia;

• Chapter 3: Status and accomplishments of 

current Federal monitoring, assessment, and 

research activities related to hypoxia, including 

research on coastal ecosystems and their 

watersheds that provides the basis for effective 

management actions;

• Chapter 4: Directions for future science activities 

and opportunities to increase effectiveness and 

cost-efficiency through coordination of programs 

across Federal agencies; 

• Appendix I: Federal Government Hypoxia or 

Hypoxia-related Research; 

• Appendix II: Case studies that feature coastal 

ecosystems across the United States affected 

by hypoxia. The featured systems were 

selected to illustrate the range of circumstances 

causing hypoxia as well as the range in status 

of scientific understanding and management 

approaches being implemented (the case studies 

are referenced throughout the report); and

• Appendix III: Details on U.S. coastal systems 

affected by hypoxia.

1.3. The Report 

Development Process

This report was prepared by a task force 

associated with the IWG-4H that included 

representatives of Federal agencies participating 

in the science and management of coastal hypoxia. 

Box 2. Legislation Relevant to 

Hypoxia 

• Harmful Algal Bloom and Hypoxia Research 

and Control Act

• Coastal Zone Management Act 

• Water Resources Development Act

• Clean Water Act

• Food, Conservation, and Energy Act of 2008 

• Energy Independence and Security Act of 

2007

• Annual appropriations of Federal agencies
Scientific Assessment of Hypoxia in U.S. Coastal Waters 9

Legislative Background and Report Process

It builds on earlier reports to assess hypoxia in 

U.S. coastal waters by updating the assessments 

and summarizing the major advances in hypoxia 

research during the past five years. Specifically, 

this report draws on An Assessment of Coastal 

Hypoxia and Eutrophication in U.S. Waters

(CENR 2003), which was called for in HABHRCA 

1998. This report also recommends priorities for 

future hypoxia-related research across the U.S. 

government.

Scientific Assessment of Hypoxia in U.S. Coastal Waters 11

2.1. The Issue of Hypoxia 

Hypoxia, or water with dissolved oxygen that is too low to support fish and other 

important species (Box 3), has been recognized as 

one of the most important water quality problems 

worldwide (Diaz and Rosenberg 2008). Hypoxia 

has become a serious problem along all of the 

Nation’s coasts and in the Great Lakes. Hypoxic 

areas are often termed “dead zones” since the 

only organisms that thrive there are those that can 

live with little or no oxygen, often only bacteria. 

Most mobile organisms are able to avoid hypoxic 

waters by swimming or crawling away; organisms 

unable to move or those trapped within a zone 

of hypoxia become physiologically stressed and 

die if exposure is prolonged or severe (Diaz and 

Rosenberg 1995, Vaquer-Sunyer and Duarte 2008).

Most coastal hypoxia is associated at the global 

scale with either areas of high population density 

or developed watersheds that 

export large quantities of 

nutrients and organic matter 

(Figure 1, Rabalais et al. 2007, 

Galloway et al. 2008, Diaz and 

Rosenberg 2008). The number 

of waterbodies with recorded 

and published accounts of 

low dissolved oxygen from 

around the globe has increased 

about an order of magnitude 

during the last 50 years, from 

less than 50 in the 1960s to 

about 400 by 2008 (Diaz 

and Rosenberg 2008). The 

number of waterbodies in the 

United States with documented 

hypoxia followed the same 

trend, increasing from 12 prior 

Causes and Status of Hypoxia 

in U.S. Coastal Waters

Chapter 2

to 1960 to over 300 by 2008 (Appendix III; Figure 

2). 

The second largest eutrophication-related 

hypoxic area in the world (after the Baltic Sea, 

which is approximately 80,000 square kilometers, 

or km2

, Karlson et al. 2002, Hansen et al. 2007) 

occurs in the United States, and is associated with 

the discharge from the Mississippi/Atchafalaya 

Rivers in the northern Gulf of Mexico. The Gulf 

of Mexico hypoxic area is similar in extent and 

volume to another large hypoxic area associated 

with China’s Changjiang River outflow (13,700 

km2

 in 1999, Li et al. 2002). The northern Gulf of 

Mexico hypoxic area has increased substantially 

in size since the mid-1980s when it was first 

measured at about 4,000 km2 (Rabalais et al. 2007). 

In 2008, it encompassed 20,719 km2

, the second 

largest area on record (http://www.gulfhypoxia.

net/). A concerted Federal interagency and multiBox 3. Hypoxia 

Definition

Hypoxia means “low oxygen”. 

In aquatic and marine systems, 

low oxygen generally refers to a 

dissolved oxygen concentration less 

than 2 to 3 milligrams of oxygen per 

liter of water (mg/L), but sensitive 

organisms can be affected at higher 

thresholds (4.5 mg/L). A complete 

lack of oxygen is called anoxia. 

Hypoxic waters generally do not 

have enough oxygen to support 

fish and other aquatic animals, and 

are sometimes called dead zones 

because the only organisms that 

can live there are microbes. The 

criteria set for health of various 

species in Chesapeake Bay are a 

good example of how one definition 

for hypoxia is not possible (EPA 

2003).
12 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

state effort has been underway since 2000 to find 

ways to reduce the size of the hypoxic area (CENR 

2000, U.S. EPA 2007; see Gulf of Mexico Case 

Study, Appendix II). 

Much of the scientific interest and management 

concern about hypoxia is focused on its principal 

cause, eutrophication, which is defined as “an 

increase in the rate of supply of organic matter to 

an ecosystem” (Nixon 1995). Eutrophication is 

most often associated with nutrient enrichment of 

coastal waters from urban and agricultural land 

runoff, wastewater treatment plant discharges, 

and air deposition of nutrients (Bricker et al. 

2007, Galloway et al. 2008) (see Section 2.3.2). 

The combination of stressors associated with 

eutrophication, which includes both HABs 

and hypoxia, continues to degrade U.S. coastal 

waters, estuaries, and the Great Lakes. Nutrient 

management, primarily via improved treatment of 

industrial and municipal point source discharges, 

has reduced hypoxia in some systems (e.g., Los 

Angeles Harbor, Delaware River, and Hillsborough 

Bay in Florida). However, a concerted and 

sustained effort to address nonpoint sources of 

nutrients will be needed to allow more waterbodies 

to recover and to protect our estuarine and coastal 

resources for the future.

2.2. Status of Hypoxia in 

the United States

Hypoxia is a serious problem in estuarine and 

coastal areas of the United States resulting from 

a diverse set of causes, including eutrophication 

driven mainly by nonpoint sources of nutrients 

(Diaz and Rosenberg 2008). The present day 

status of hypoxia contrasts with that of fifty 

years ago when it was primarily a problem in 

rivers resulting from inadequate treatment of 

municipal and industrial wastes. Through the 

1970s, organic matter loading from sewage and 

industrial discharges was the most salient cause 

of eutrophication and hypoxia in the United 

States (Smith et al. 1987). The majority of the 69 

hypoxic U.S. waterbodies known from that time 

period were related to discharges from wastewater 

treatment (e.g., Providence River, Melrose et al. 

2007) or industry (e.g., Pensacola Bay, Hagy and 

Murrell 2007). Actions following the passage 

of the Clean Water Act in 1972 reduced these 

point source organic loads and, much later, began 

to reduce point source phosphorus and (even 

later) nitrogen loading, contributing to some 

improvements in low dissolved oxygen problems. 

The Clean Water Act, however, did not explicitly 

address management and regulation of nonpoint 

Figure 1. Global distribution of systems affected by low dissolved oxygen. 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 13

The Problem of Hypoxia in U.S. Waters

sources of pollutants. It was in the 1970s that 

the rising effects of nonpoint runoff of nutrients 

were observed in water quality deterioration 

around the United States (Smith et al. 1987). The 

1970s were also when first reports of hypoxia 

appeared for our larger coastal systems (northern 

Gulf of Mexico, New York Bight, Long Island 

Sound). By the 1980s, it became apparent that 

increasing nutrient loads from nonpoint sources 

were responsible for an expansion of eutrophic 

conditions in estuarine and coastal systems within 

the United States (reviewed by Bricker et al. 

1999, 2007). Overall, the United States has led a 

global trend in which agricultural fertilizers are the 

leading nonpoint source of nutrient pollution, but 

atmospheric deposition from burning of fossil fuels 

and nitrogen fixation associated with legume crops 

also contribute significantly (Howarth et al. 1996).

The primary sources of nutrient pollution vary 

substantially among watersheds (e.g., Figure 3), 

complicating the task of nutrient management.

A current analysis of 647 U.S. coastal and 

estuarine ecosystems indicates that the percentage 

of systems with hypoxia has increased dramatically 

since the 1960s (Figure 2) and even since the 1980s 

(Table 1). The first national assessment of oxygen 

conditions in U.S. waters, conducted in the 1980s, 

found 38% of systems to have hypoxia (Whitledge 

1985). Subsequent eutrophication assessments 

found greater than 50% of systems to have hypoxia 

(Bricker et al. 1996, 1997a, 1997b, 1998a, 1998b, 

2007). Updating the information from all these 

sources finds that 307 of 647 ecosystems have 

hypoxia (Appendix III). Most of the increases 

since the 1980s occurred in the North Atlantic, 

South Atlantic, and Pacific regions and reflect 

an increase in the incidence of hypoxia. In the 

Middle Atlantic and Gulf of Mexico regions, the 

percentage of hypoxic systems was already high 

in the 1980s and remains high to date. Further, 

the third National Coastal Condition Report (U.S. 

EPA 2008) found water quality for Atlantic and 

Gulf coasts to range from fair to poor, based on 

data from the early 2000s. For the Great Lakes, 

there appears to have been little change in hypoxic 

conditions since the 1980s. 

Dissolved oxygen conditions have improved 

in some waterbodies due to intensive regulation 

of nutrient or carbon inputs, primarily from more 

advanced sewage and industrial treatment. The 

best examples are from smaller systems where 

point source discharges were the primary source 

of organic matter and nutrients, such as the 

Hudson River in New York and the Delaware 

River in Pennsylvania and New Jersey (Brosnan 

and O’Shea, 1996; Patrick, 1988). In larger 

systems where point sources have been intensely 

managed, dissolved oxygen conditions have not 

improved because of large nonpoint sources of 

nutrients. Examples include Chesapeake Bay 

and Lake Erie, which have a long history of 

nutrient management but continuing problems 

with large-scale hypoxia. (See Appendix II). 

Even with improved management of nonpoint 

sources, recovery of some large systems may 

be delayed due to nutrient and organic matter 

that have accumulated in the sediments over the 

years, thereby increasing oxygen demand, and, 

in turn, expanding the amount of hypoxia for a 

given load of nutrients (Turner et al. 2008). This 

 Region % Hypoxic 1980s1 % Hypoxic 1990s2 % Hypoxic 2000s3 % Hypoxic 2000s4

North Atlantic 6 (1 of 17) 22 (4 of 18) 35 (7 of 20) 26 (10 of 38)

Mid-Atlantic 50 (19 of 38) 59 (13 of 22) 64 (14 of 22) 42 (76 of 180)

South Atlantic 18 (9 of 51) 64 (14 of 22) 91 (20 of 22) 55 (77 of 139)

Gulf of Mexico 69 (38 of 55) 84 (32 of 38) 68 (26 of 38) 51 (105 of 205)

Pacific 21 (6 of 29) 26 (10 of 39) 35 (13 of 37) 46 (37 of 80)

Great Lakes 1 of 5 lakes 2 of 5 lakes 2 of 5 lakes

Total Nation 38 (73 of 190) 52 (73 of 139) 58 (80 of 139) 47 (307 of 647)

1

 Based on Whitledge 1985a; 2 Based on Bricker et al. 1996, 1997a, 1997b, 1998a, 1998b; 3 Based on Bricker et al. 2007; 4 From 

Appendix III.

Table 1. Percentage of U.S. estuaries and coastal waterbodies with reports of hypoxia.
14 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

may be the case in the northern Gulf of Mexico 

and Chesapeake Bay (Hagy et al. 2004, Turner et 

al. 2008). Unfortunately, nutrient loading from 

agricultural and atmospheric sources is predicted to 

increase globally over the next 50 years (Tilman et 

al. 2001, Galloway et al. 2008), creating additional 

stress on coastal waterbodies already in decline. 

Federal research and management actions must 

accelerate the pace of water quality management in 

order to protect and restore valued coastal aquatic 

resources. 

2.3. Causes of Hypoxia

Widespread and persistent hypoxia is generally 

not a natural condition in estuaries, coastal waters, 

or large lakes like the Great Lakes, with Lake 

Erie being an exception (Appendix II). However, 

naturally occurring oxygen depletion does occur, 

as in oceanic oxygen minimum zones, fjords, 

some stratified seas (e.g., the Black Sea), lakes and 

ponds, and swamps and backwaters that circulate 

poorly and have large loads of natural land-derived 

organic matter. Naturally occurring hypoxia is 

not the focus of this report, but it is important to 

consider these cases because human activities may 

increase the frequency, duration, and intensity of 

naturally occurring hypoxia (Cooper and Brush 

1991, Helly and Levin 2004, Diaz and Rosenberg 

2008).

When the rate of oxygen consumption in 

aquatic environments increases such that the 

oxygen consumption rate exceeds resupply, 

oxygen concentrations can quickly decline 

to levels insufficient to sustain most animal 

life. Two conditions are generally required for 

the development and maintenance of hypoxia 

(Figure 4):

• water column stratification that isolates a layer 

of bottom water and sediments from a usually 

well-oxygenated surface layer (see Section 

2.3.1), and 

• a source of organic matter, which is then 

decomposed and depletes oxygen in the isolated 

bottom layer (see Section 2.3.2). 

Diel-cycling hypoxia, where conditions can 

cycle from supersaturation of oxygen late in the 

afternoon to hypoxia or anoxia near dawn, is a 

unique situation that does not require the first 

condition described above. This phenomenon 

can occur in unstratified waters and appears to be 

increasing in frequency (D’Avanzo and Kremer 

1994, Verity et al. 2006, Shen et al. 2008). It most 

often occurs in shallow, eutrophic tidal creeks 

where oxygen exchange at the water surface 

Figure 2. Change in number of U.S. coastal areas experiencing hypoxia from 12 documented areas in 1960 to over 300 

now (Appendix III). Not shown here are one hypoxic system in Alaska and one in Hawaii.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 15

The Problem of Hypoxia in U.S. Waters

is insufficient to supply the respiratory needs 

of microbes and other organisms. This type of 

transient or diel hypoxia may cause pervasive 

impacts on living resources both because of the 

frequency with which it occurs (hours to days) 

and its location (small and shallow nursery ground 

habitats, e.g., Pepper Creek, Delaware; Tyler and 

Targett 2007, Tyler et al. 2008). The increased 

production of organic matter within a system, 

mostly in the form of phytoplankton productivity 

in response to anthropogenic nutrient pollution, 

contributes to both seasonal and diel-cycling 

hypoxia in coastal ecosystems. In shallow systems 

that are highly eutrophic, calm weather conditions 

and extended periods of cloud cover can cause low 

dissolved oxygen events (Tyler et al. 2008).

Whereas physical factors create the physical 

conditions that are usually necessary for hypoxia 

to develop in bottom waters, nutrient-driven 

eutrophication provides the increased deposition of 

decomposing organic matter to the bottom layer, 

creating increased oxygen demand. Although 

physical factors can change over the long-term, 

they have not in most cases (e.g., Hagy et al. 

2004, Greene et al. 2009). Thus, eutrophication is 

the principal cause of the long-term increases in 

hypoxia that have been observed. 

2.3.1. Physical Factors

Density stratification of the water column, in 

which a less dense layer of water floats on top 

of a denser bottom layer, is an almost universal 

characteristic of coastal systems subject to seasonal 

bottom water hypoxia. Stratification reduces 

the potential for oxygen from the atmosphere to 

replenish oxygen depleted at depth. In most cases 

involving marine systems, a vertical gradient of 

salinity, creating a halocline, is the most important 

factor contributing to density stratification. 

Surface heating, creating warmer surface water 

temperatures and thus a vertical gradient of 

temperature, or a thermocline, is the cause of 

stratification in lakes and can also contribute to 

density stratification in marine systems, especially 

during spring when deeper waters are relatively 

cold. Thermal stratification creates the potential 

for hypoxia in Lake Erie and is also known to be 

important in Long Island Sound and New York 

Bight (Boesch and Rabalais 1991, Hawley et al.

2005, Lee and Lwiza 2008). In the fall, cooling 

temperatures and decreasing freshwater inputs 

can destabilize summer stratification, leading to 

relatively abrupt mixing or “turnover” of the water 

column that eliminates seasonal hypoxia. Fall 

turnover is often associated with a wind event such 

as a storm or frontal passage.

Urban/Suburban

Agriculture

Atmospheric

Chesapeake Bay

Urban/Suburban

Agriculture

Atmospheric

Urban/Suburban

Agriculture

Atmospheric

Narragansett Bay

Urban/Suburban

Agriculture

Atmospheric

Agriculture

Atmospheric

Urban/Suburban

Pasture

Gulf of Mexico

Urban/Suburban

Pasture

Gulf of Mexico

Figure 3. Comparison of the relative contribution of major sources of nitrogen pollution in three coastal ecosystems 

experiencing hypoxia. Urban/suburban includes both point (industrial and sewage effluent) and nonpoint sources (residential run 

off). Data sources: Chesapeake Bay: Chesapeake Bay Program; Narragansett Bay: Nixon et al. 2008, Moore et al. 2004; Gulf of 

Mexico: Alexander et al. 2008. 

Chesapeake Bay Narragansett Bay Gulf of Mexico
16 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

In river-dominated estuaries and ocean margins, 

density stratification and other circulation features 

are strongly affected by the amount of less dense 

freshwater flowing out of associated rivers. 

Therefore, the extent and severity of seasonal 

hypoxia varies on an annual basis in relation to 

the magnitude of freshwater inputs. In larger 

systems, where freshwater is retained in the system 

for longer periods of time, summer hypoxia is 

usually coupled most closely to freshwater inputs 

during spring, when spring rains or snow melt 

cause high freshwater flow (e.g., Chesapeake 

Bay, Hagy et al. 2004; northern Gulf of Mexico, 

Greene et al. 2009). In smaller systems, physical 

conditions conducive to development of hypoxia 

may be coupled to freshwater inputs on a shorter 

time scale. For example, a single early fall pulse 

of freshwater associated with Hurricane Ivan 

stimulated development of an unseasonable period 

of hypoxia in Pensacola Bay, Florida, during 

fall 2004 (Hagy et al. 2006). Shen et al. (2008) 

observed periods of hypoxia lasting two to five 

days in a shallow mid-Atlantic creek following a 

rain event.

Development and maintenance of hypoxia are 

strongly affected by water column mixing. Strong 

tidal mixing prevents water column stratification 

almost entirely in some systems. Where tides are 

not as strong, low dissolved oxygen events may 

occur during neap tides, the phase of the springneap tidal cycle when tidal mixing is minimal 

(Haas 1977). Stratification, and thus vulnerability 

to hypoxia, is reduced during the larger spring 

tides, which are associated with full and new 

moons, when tidal currents are stronger and 

generate increased mixing of the water column. 

Some estuaries, such as Mobile Bay, Alabama, 

Figure 4. Conceptual diagram illustrating development and effects of hypoxia in stratified waters (from Downing et al. 

1999). The pycnocline is the boundary that stratifies and separates the bottom and surface water layers.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 17

The Problem of Hypoxia in U.S. Waters

and Pensacola Bay, Florida, in the northeastern 

Gulf of Mexico have low amplitude tides (Hagy 

and Murrell 2007), and others, such as the 

Albermarle-Pamlico Estuarine System on the North 

Carolina coast, are virtually tideless (Luettich 

et al. 2002). These estuaries, which are also in 

a warmer climate that yields higher respiration 

and nutrient regeneration rates, are particularly 

susceptible to stratification and hypoxia. Wind is 

an especially important factor affecting hypoxia in 

these microtidal estuaries (Reynolds-Fleming and 

Luettich 2004, Park et al. 2007, Hagy and Murrell 

2007). 

2.3.2. Biological/chemical Factors

Eutrophication, fundamentally a biological 

and biogeochemical process, is an important 

factor and indeed the principal cause of coastal 

hypoxia. In an update to the National Estuarine 

Eutrophication Assessment (Bricker et al. 2007, 

See Table I), eutrophication was recognized as a 

widespread problem, with 65% of assessed systems 

(99 of 141 systems had adequate data for analysis) 

showing moderate- to high-level problems. The 

most commonly reported eutrophication-related 

problems included hypoxia, losses of submerged 

grasses, excessive algal blooms (the most 

commonly reported problem), and numerous 

occurrences of nuisance and toxic HABs. The midAtlantic was identified as the region most impacted 

by eutrophication. The majority (almost 60%) of 

estuaries assessed, with the exception of North 

Atlantic systems (Cape Cod north to Maine), were 

highly influenced by human-related activities that 

contributed to land-based sources of nutrient loads. 

The most commonly reported causes of nutrientrelated impairments were agricultural activities 

(row crops and livestock operations), wastewater 

treatment plants, urban runoff, and atmospheric 

deposition. Eutrophication-related problems were 

predicted to worsen in 65% of estuaries, whereas 

19% of the assessed estuaries were expected to 

improve in the future. Analysis of the extent 

of change in 58 estuaries from the early 1990s 

to the early 2000s shows that most (55%) were 

unchanged, including all of the larger estuaries. 

The principal sources of nutrients that sustain 

coastal eutrophication vary among systems. Where 

significant rivers enter the coastal zone, nutrient 

loads associated with the freshwater discharge are 

usually the predominant source. Coastal systems 

lacking substantial riverine inputs may receive a 

substantial fraction of nutrient inputs via submarine 

groundwater discharge or direct atmospheric 

deposition, as in Barnegat Bay, New Jersey 

(Kennish et al. 2007). The major anthropogenic 

sources of nutrients to coastal waters are row 

crop agriculture and animal operations, industrial 

and municipal wastewater discharges, nonpoint 

source runoff from urban and suburban areas, 

and atmospheric deposition (Figure 3). Human 

activities have been linked to a dramatic increase 

in nitrogen cycling in the natural environment. 

Watersheds can become “nitrogen-saturated”, 

for example, when further additions of nitrogen 

do not elicit a response from the ecosystem. In 

nitrogen-saturated watersheds, the surplus nitrogen 

will theoretically leak to streams, groundwater, 

or the atmosphere (Vitousek et al. 1997). Loss or 

degradation of riverine and coastal wetlands can 

also contribute to eutrophication of coastal waters 

because wetlands naturally trap and retain nutrients 

(e.g., Valiela and Cole 2002). 

In most cases, eutrophication has been caused 

by an anthropogenic increase in nutrient inputs. In 

a few cases, large but, nonetheless, natural sources 

of nutrients have been implicated in sustaining 

high primary productivity in coastal systems. For 

example, some watersheds in southwest Florida 

have naturally high concentrations of phosphates 

that can support high levels of primary production 

(Turner et al. 2006a). Natural upwelling of 

nutrient-rich deep ocean water into shallow areas 

also can support large blooms of phytoplankton 

(Glenn et al. 1996, Chan et al. 2008) and can 

result in hypoxia. Upwelling of nutrient-rich 

waters has been implicated in the development of 

severe widespread hypoxia and, for the first time 

(in 2006), anoxia on Oregon’s inner continental 

shelf (Grantham et al. 2004, Chan et al. 2008). 

Transport of hypoxic water from the continental 

shelf into coastal embayments has also been 

documented along the Oregon coast (Brown 
18 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

et al. 2007). These developments seem to be 

linked to impacts of climate variation on ocean 

processes, such as intensity of upwelling winds, 

oxygen concentration in upwelled water, and 

water column respiration (Grantham et al. 2004, 

Chan et al. 2008). More subtle upwelling has 

been observed along the New Jersey coast and 

has been implicated in development of nearshore 

hypoxia (Glenn et al. 1996, 2004). Both of these 

cases, however, contrast with the situation for most 

coastal areas undergoing eutrophication, where the 

source of increased nutrient input is land-based and 

attributable to anthropogenic causes. 

Hypoxia can be related in some cases to 

documented long-term increases in algal 

biomass. For example, the long-term increase in 

chlorophyll-a (a proxy for phytoplankton biomass) 

in the Chesapeake Bay, as documented by Harding 

and Perry (1997), was concurrent with the increase 

in hypoxia documented by Hagy et al. (2004). In 

a few cases, hypoxic events have been related to 

high biomass HABs. For example, the one-time 

hypoxic event in the New York Bight (Garlo et al. 

1979, Boesch and Rabalais 1991) and hypoxia in 

the Peace River-Charlotte Harbor system (Turner et 

al. 2006a) were both related to high biomass algal 

blooms. Further, massive mortalities of bottomdwelling organisms were associated with the 

cascading effects of algal toxicity, hypoxia, anoxia, 

and hydrogen sulfide poisoning during a toxic HAB 

event in Florida in 2005 (Landsberg et al. 2009).

2.4. Consequences of 

Hypoxia

2.4.1. Ecological Consequences

Ecological effects of hypoxia in coastal systems 

can vary in both degree and scale (Figure 5). The 

specific concentration of dissolved oxygen below 

which various animals suffocate varies, but for 

estuarine and marine species, effects generally 

appear when oxygen drops below about 3 mg/L 

(Diaz and Rosenberg 1995, Ritter and Montagna 

1999, Rabalais et al. 2001, Breitburg et al. 2001, 

Karlson et al. 2002). However, the behavior 

of some organisms (e.g., fish, larvae) can be 

negatively affected at oxygen concentrations as 

high as 4-4.5 mg/L (Whitmore et al. 1960, Kramer 

1987, Breitburg 1994). Toxic hydrogen sulfide 

is often present in waters nearly or completely 

devoid of oxygen and significantly reduces survival 

(Gamenick et al. 1996).

Fish kills are an obvious and very unpleasant 

consequence of hypoxia. The frequency and 

magnitude of fish kills have increased as nutrientrelated eutrophication has worsened both hypoxia 

and HABs (Thurston 2002, Thronson and Quigg 

2008). Fish kills related to hypoxia have been 

noted in waterbodies on all U.S. coasts, but the 

incidence of fish kills does not capture the extent 

of hypoxia impacts. Fish kills are much less 

widespread than hypoxia itself and sometimes 

occur only when several factors are present along 

with hypoxia (e.g., HABs as in Corsica River, 

Maryland, Bricker et al. 2007) or when hypoxia 

develops in a way that prevents fish from escaping. 

Other effects of hypoxia are less obvious, but 

more pervasive and likely more important overall. 

These include shifts in spatial distribution of 

organisms, changes in community structure caused 

by emigration of fish and mobile invertebrates, 

Figure 5. The range of ecological impacts exhibited as 

dissolved oxygen levels drop from saturation to anoxia 

(based on Diaz and Rosenberg 1995, Rabalais et al. 2001).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 19

The Problem of Hypoxia in U.S. Waters

mortality of sessile (immobile) 

bottom-dwelling organisms, 

and alteration or blockage of 

normal migration routes of 

fish and invertebrates. 

Hypoxic habitats that are 

avoided by organisms are 

functionally lost from the 

system (Breitburg 2002, 

Rabalais and Turner 2001, 

Sagasti et al. 2001). Because 

oxygen thresholds for 

avoidance are usually higher 

than for survival (Figure 5), 

habitat loss due to hypoxia 

is far greater than would be 

suggested by calculations based on recruitment 

or survival tolerances. Changes in community 

structure and habitat loss associated with hypoxia 

can also propagate to other components of the food 

web. For example, impacts to animals that act as 

crucial food web linkages between algal producers 

and top predators (e.g., benthic suspension feeders) 

result in a decreased flow of energy to predators 

and an increase to microbes (Figure 6, Diaz and 

Rosenberg 2008). Avoidance of hypoxia can also 

reduce energy flow to predators. Hypoxia can 

cause reduced growth (Taylor and Miller 2001), 

lower reproduction (Marcus et al. 2004), and other 

physiological effects (Wu et al. 2003). Shrimp 

and crabs exposed to hypoxia, for example, 

become immunocompromised and may suffer 

increased susceptibility to disease and mortality 

from bacterial infections (Le Moullac et al. 1998, 

Holman et al. 2004, Burgents et al. 2005; Tanner et 

al. 2006). 

Hypoxia has contributed to the collapse or 

impairment of a number of commercially important 

fisheries worldwide, including Norway lobster 

in the Kattegat Sea (Baden et al. 1990) and 

bottom-dwelling fish in the Baltic and Black Seas 

(Breitburg et al. 2001, Mee 2006). Effectively 

separating impacts of hypoxia on exploited fishery 

populations from those due to overfishing can be 

challenging (Breitburg et al. 2009). Most likely, 

the effect of hypoxia is to decrease productivity 

and resilience of exploited populations, making 

them more vulnerable to collapse in the face of 

heavy fishing pressure.

The ecological impacts of hypoxia may be 

understood in terms of the ecosystem services 

normally provided by a healthy ecosystem, but lost 

as a result of hypoxia (Table 2). A full assessment 

of ecosystem services lost helps bridge the gap 

between ecological functions lost and their impact 

on people. In some cases, though not without 

challenges, ecosystem services can be assigned a 

reasonable dollar value. In these cases, analysis 

of services helps convey the economic costs 

associated with ecological impacts. 

Fisheries yield is one ecosystem service that 

can be impacted both directly and indirectly by 

hypoxia. Mortality of fisheries species is a direct 

mechanism by which services are lost. Loss of 

forage for bottom-feeding fish and shellfish due to 

hypoxia is probably more important in most cases 

and also amounts to a loss of ecosystem services. 

In the Chesapeake Bay, seasonal hypoxia lasts 

about three months and reduces the Bay’s total 

benthic secondary production by about 5% (Diaz 

and Schaffner 1990), or roughly 75,000 metric 

tons of biomass (Diaz and Rosenberg 2008). This 

is enough to feed about half the annual blue crab 

catch for a year. In the northern Gulf of Mexico, 

severe seasonal hypoxia can last up to six months 

and reduces benthic biomass by about 212,000 

metric tons when the hypoxic zone is 20,000 km2

(Rabalais et al. 2001). This lost biomass could 

Figure 6. Conceptual view of how hypoxia alters ecosystem energy flow with 

example systems (modified from Diaz and Rosenberg 2008).
20 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

feed about 75% of the brown shrimp catch for a 

season (Diaz and Rosenberg 2008). It is unknown 

whether these systems can recover secondary 

production lost to hypoxia during periods with 

normal oxygen levels. The Chesapeake Bay has 

a recovery period of approximately nine months, 

whereas the northern Gulf of Mexico requires six 

months for recovery of the lost benthic production. 

Well-oxygenated conditions outside of summer, 

however, may be inadequate to support recovery 

since many other growth requirements (especially 

appropriate water temperatures) are optimal in the 

summer. 

One of the less obvious ecosystem services lost 

during hypoxia is sediment mixing by benthic 

organisms, or ‘bioturbation.’ Reworking of 

sediments via bioturbation promotes oxygenation 

of sediments, improving habitat for benthic 

animals and promoting biogeochemical feedback 

processes that reduce nutrient recycling and 

limit eutrophication. In particular, bioturbation 

promotes coupled nitrification and denitrification, 

which eliminates excess bioavailable nitrogen from 

the ecosystem. Loss of these services amounts to 

additional nitrogen loading, which must be offset 

by additional controls on inputs (Hagy et al. 2004). 

When bioturbation is eliminated due to hypoxia, 

nitrogen is returned to the water as bioavailable 

ammonium, often with phosphorus as well, 

reinforcing a cycle of eutrophication (Aller 1994, 

Kemp et al. 2005).

Determining the ecological consequences of 

hypoxia on ecosystem services (Table 2) is often 

complicated by cumulative and interacting impacts 

involving a variety of stressors. Quantification of 

the relationship between hypoxia and impacts on 

Impacts on Ecosystem Services Example Reference

Loss of biomass

Direct mortality of fisheries species Long Bay Koepfler et al. 2007

Direct mortality of prey species Northern Gulf of Mexico Rabalais et al. 2001

Reduced growth and production Chesapeake Bay Diaz and Schaffner 1990

Reduced recruitment Patuxent River Breitburg 1992

Loss of biodiversity

Elimination of sensitive species Pensacola Bay Hagy et al. 2006

Reduced diversity Pamlico River Tenore 1972

Increased susceptibility to disease and other stressors St. Johns River Mason 1998

Lower food web complexity Neuse River Estuary Baird et al. 2004

Loss of habitat

Crowding of organisms into suboptimal habitats Neuse River Estuary Eby et al. 2005

Increased predation risks (both natural and fishing) Northern Gulf of Mexico Craig and Crowder 2005

Forced migration from preferred habitat St. Josephs Bay Leonard and McClintock 1999

Altered or blocked migration routes New York Bight Sindermann and Swanson 

1980

Altered energy and biogeochemical cycling

Increased energy flow through microbes Corpus Christi Bay Montagna and Ritter 2006

Production of toxic hydrogen sulfide Dead end canals Luther et al. 2004

Release of phosphorus from sediments Lake Erie Hawley et al. 2006

Release of ammonia and ammonium from sediments Chesapeake Bay Cowan and Boynton 1996

Loss of denitrification Chesapeake Bay Lewis et al. 2007

Table 2. Principal ecosystem characteristics and services impacted by hypoxia. Ecosystem 

services are processes by which the environment produces resources that are important 

to humans. Lost ecosystem characteristics highlighted here are critical for supporting 

ecosystem services. Not listed here are impacts to aesthetics or services lost due to 

eutrophication in general.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 21

The Problem of Hypoxia in U.S. Waters

commercial and recreational living resources are 

needed by managers in order to improve coastal 

management and policy decision-making. Recent 

research advances in this area are discussed in 

Section 3.2.

2.4.2. Economic Consequences

There is a growing collection of literature on the 

ecological consequences of hypoxia, but economic 

evaluations are lacking. Economic effects 

attributable to hypoxia are subtle and difficult 

to quantify even when mass mortality events 

occur. Much of the problem is related to multiple 

stressors (habitat degradation, overfishing, HABs, 

and pollution) acting on targeted commercial 

populations as well as factors that impact fishers’ 

economics (aquaculture, imports, economic costs 

of fishing, and fisheries regulations). Economic 

impacts that stem from the effects of hypoxia 

on fishery stocks are mostly subtle and tied to 

ecological impacts through reduced growth and 

reproduction. Other economic costs imposed on 

fishers are related to increased time on fishing 

grounds and costs of searching for stocks (e.g., to 

reach more distant fishing grounds beyond areas 

impacted by hypoxia). How these costs translate 

to impact on profits is complex, however, because 

in addition to the ramifications of reduced quantity, 

the unit value of landings on the market affects its 

total value and must be considered when evaluating 

the economic impacts. 

Although quantifying costs of hypoxia-related 

mortality events is difficult, there are some 

published examples (Table 3). Hypoxia in the 

early 1970s in Mobile Bay, Alabama was estimated 

to have killed over $500,000 worth of oysters 

(May 1973). An even greater economic cost was 

associated with the declining stock size associated 

with mortality and poor recruitment of oysters 

in years with severe hypoxia. A modeling study 

in the Patuxent River in Maryland estimated that 

the net value of striped bass fishing alone would 

decrease over the long-term by over $145 million 

if the entire Chesapeake Bay were impacted by 

hypoxia, which would preclude fishing in other 

sites (Lipton and Hicks 2003). Impacts of hypoxia 

on the overall health of the striped bass population 

and impacts to other Chesapeake fisheries were not 

included in this estimate but would substantially 

Event Impacts considered 

in Estimate

Estimated Economic 

Impact 

Economic Impact in 

2009 dollars

Hypoxia in Mobile Bay in 

1970’s (May 1973)

Mortality to oysters $500,000 $2,400,000

Modeled hypoxia 

in Patuxent River, 

Maryland (Lipton and 

Hicks 2003)

Striped bass fishing and 

associated activities in 

Patuxent River*

$100,000** for dissolved 

oxygen below 5 mg/L in 

the River

$300,000** for anoxia in 

the River

$145,000,000** for 

dissolved oxygen less 

than 3mg/L in entire 

Chesapeake Bay 

(eliminates substitute 

fishing sites) 

$110,000** 

$340,000** 

$166,000,000**

New York Bight hypoxic 

event in the summer of 

1976 (Figley et al. 1979)

Surf clams, finfishes, 

ocean quahogs, sea 

scallops, lobsters

$70,000,000 $265,000,000

 * Note that the impact would be substantially greater if all target species were considered.

**Net present value; the net present value represents the chronic effects of hypoxia on the value of striped bass 

fishing.

Table 3. Examples of hypoxia-related economic impacts. For a current perspective, impacts 

are also shown in 2009 dollars, calculated from the original values using the consumer price 

inflation index (http://www.bls.gov/cpi/).
22 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

Climate Driver Direct Effect Secondary Effect Influence on 

Hypoxia

Increased 

temperature

 

More evaporation Decreased stream flow -

Land-use and cover changes +/-

Less snow cover More nitrogen retention -

Warmer water Stronger stratification +

Higher metabolic rates +

More precipitation More stream flow Stronger stratification +

More nutrient loading +

More extreme rainfall Greater erosion of soil phosphorus +

Less precipitation Less stream flow Weaker stratification -

Less nutrient loading -

Higher sea level Greater depth Stronger stratification +

Greater bottom water volume -

Less hydraulic mixing +

Less tidal marsh Diminished nutrient trapping +

Summer winds and 

storms

Weaker, less water 

column mixing

More persistent stratification +

Stronger, more water 

column mixing

Less persistent stratification -

Shifting wind patterns Weaker/stronger upwelling potential +/-

Table 4. Estimated influence of climate drivers on the extent and severity of hypoxia 

(+ = more hypoxia) (Diaz 2008, Modified from Boesch et al. 2007). 

increase the overall economic consequences to 

fishers in the region. During the 1976 summer 

hypoxic event in the New York Bight, acute 

economic losses were estimated to have been over 

$70 million (Figley et al. 1979). Much of this 

loss was due to impacts to the surf clam resource, 

accounting for more than $60 million. These 

values consider short-term impacts from actual 

losses reported by fishers and potential losses due 

to resource mortality.

Experience with hypoxic zones around the globe 

shows that both ecological and fisheries impacts 

become progressively more severe as hypoxia 

worsens (Diaz and Rosenberg 1995, Caddy 

1993) and the area of suitable habitat declines 

(Bricker et al. 2006). Large systems around 

the globe have suffered serious ecological and 

economic consequences from seasonal hypoxia; 

most notably the Kattegat and the Black Sea. 

Consequences range from localized loss of catch 

and recruitment failure to complete system-wide 

loss of fishery species (Karlsen et al. 2002, Mee 

1992). In systems where habitat is only partially 

lost to hypoxia, such as Long Island Sound and the 

Chesapeake Bay, catch rates for recreational fishing 

decline (Bricker et al. 2006).

2.5. Future Considerations

2.5.1. Climate change 

Climate change will almost certainly influence 

both naturally occurring and eutrophicationrelated hypoxia, as well as the incidence of other 

ecological problems, such as HABs. To fully 

understand environmental change, it is necessary to 

consider the influence of multiple climate drivers 

(Table 4). In general, the expected long-term 

ecological changes favor progressively earlier onset 

of hypoxia each year and, possibly, longer overall 

duration (Boesch et al. 2007). 

Increasing average water temperature is one 

mechanism by which climate change may increase 

susceptibility of systems to hypoxia. Higher water 

temperatures promote increased water column 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 23

The Problem of Hypoxia in U.S. Waters

stratification, decreased solubility 

of oxygen, and increased metabolic 

rates, including oxygen consumption 

and nutrient recycling. Climate 

predictions also suggest large 

changes in precipitation patterns, 

but with significant uncertainty 

regarding what changes will occur 

in any given watershed (Christensen 

et al. 2007). Increased precipitation 

can be expected to promote 

increased runoff of nutrients to 

estuarine and coastal ecosystems 

and increased water column 

stratification within these systems, 

contributing to more severe oxygen 

depletion (Table 4, Global Climate 

Change Impacts in the U.S. 2009, 

Justic ́ et al. 2007, Najjar et al. 

2000). Climate predictions for the 

Mississippi River basin suggest 

a 20% increase in river discharge 

(Miller and Russell 1992), which is expected to 

increase the average extent of hypoxia on the 

northern Gulf of Mexico shelf (Greene et al. 2009). 

Climate-associated changes in oceanic wind 

patterns can impact ocean circulation at a large 

scale. The severe hypoxia that has developed every 

year since 2002 along the coast of Oregon has been 

linked to climate-based changes in regional wind 

patterns, which affect water column stratification 

and delivery of nutrients from deep water to 

relatively shallow coastal areas. 

2.5.2. Impacts of Biofuels Strategy 

The EISA of 2007 mandates production of 

36 billion gallons of biofuels by the year 2022, 

with a 15 billion gallon limit for the amount to 

come from corn. Compared to other potential 

sources of biomass for biofuel production, such as 

perennial grasses or soybeans, corn is less efficient 

at taking up applied nutrients and usually requires 

higher nutrient application rates—these factors 

contribute to higher nutrient loadings (especially 

nitrogen) with corn (CBC 2007, NRC 2007). 

Increased production of corn-based ethanol biofuel 

is projected to exacerbate hypoxia in the Gulf 

of Mexico and other coastal areas (Greene et al. 

2009, Rabalais et al. 2009). Donner and Kucharik 

(2008) estimate that expanded corn cultivation 

will increase the average annual flux of dissolved 

inorganic nitrogen to the Gulf of Mexico by 10-

34%. The acreage planted in corn grew by 19% 

between 2006 and 2007, replacing acreage in 

conservation reserve programs as well as soybeans 

and cotton (crops that are frequently less nitrogenintensive, particularly in the Upper Midwest; 

see Potter et al. 2006) (Turner et al. 2008, NASS 

2007). However, this increase did not continue 

as high fertilizer prices, favorable prices for other 

crops, and a return to normal crop rotations led to 

a 7% decline in corn production in 2008 (NASS 

2008). The EISA mandates that the U.S. biofuels 

strategy be ‘sustainable.’

2.5.3. Impacts of Future Management 

Decisions

The extent of hypoxia in the future will 

depend on land management practices including 

agricultural practices.. Climate change will 

affect water column stratification, organic matter 

production, nutrient discharges, and rates of 

oxygen consumption. Land management will 

Figure 7. Relative magnitude and contribution (the larger the arrow, the 

larger the contribution) of land management practices versus climate change 

factors to expansion or contraction of low dissolved oxygen (modified from 

Diaz and Breitburg 2009).
24 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 2

affect nutrient budgets and concentrations of 

nutrients applied to land through agriculture 

(Figure 7). For example, the expansion of 

agriculture for production of crops to be used 

for food and biofuels will, lacking preventive 

actions, result in increased nutrient loading to 

coastal waters and increased eutrophication effects 

(U.S. EPA 2007, Rabalais et al. 2007). On the 

other hand, improved agricultural conservation 

practices and large-scale implementation of 

nutrient best management practices (BMPs) can 

create dramatically better outcomes for water 

quality. The development of cellulosic ethanol 

production will enable farmers and forest managers 

to derive income from their lands while reducing 

nutrient runoff. This is an important aspect of 

the plans to achieve water quality improvements 

in the Chesapeake Bay region (Chesapeake Bay 

Commission and Commonwealth of Pennsylvania 

2008). Application of these alternatives on 

agricultural lands that contribute disproportionately 

high nitrogen loads (e.g., tile-drained fields) will 

be especially beneficial. More widespread and 

aggressive implementation of nutrient removal 

technologies in wastewater and stormwater 

management also offers opportunities to reduce 

nutrient enrichment, eutrophication, and hypoxia. 

Together, comprehensive nutrient management 

has the potential to offset the impact of human 

population pressure, which otherwise will likely 

continue to be the main driving factor in the 

persistence and spreading of coastal hypoxia. 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 25

Federal Hypoxia and 

Watershed Science Research: 

Status and Accomplishments

Chapter 3

The serious and complex environmental issue of hypoxia and eutrophication cannot be 

studied or managed by any one Federal or state 

agency, but requires an organized, comprehensive 

approach. This chapter highlights Federal 

research accomplishments since 2003 when the 

last HABHRCA-mandated hypoxia assessment 

was compiled (CENR 2003). The Federal 

research presented herein is integral for informed 

decision-making and successful management of 

nutrients and hypoxia in an “adaptive management 

framework” (Figure 8). 

Under this framework, current scientific 

knowledge guides development of management 

goals with the option to continue to assess 

knowledge gaps. As scientific understanding 

advances, management goals are reassessed 

and adjusted as needed. Approaches taken in 

the Gulf of Mexico (Box 4), Chesapeake Bay 

(Box 5), and Long Island Sound (Box 6) provide 

good examples of the use of science to inform 

management decisions. In addition, regional 

governance structures involving multiple state 

and Federal partners are emerging as an important 

mechanism for mitigating hypoxia because most 

cases of coastal hypoxia are linked to nutrient 

loads resulting from watersheds that cross state 

boundaries. Examples include the Gulf of Mexico/

Mississippi River Watershed Nutrient Task 

Force, Gulf of Mexico Alliance, Gulf of Mexico 

Program, Great Lakes Regional Collaboration, 

Figure 8. Conceptual diagram explaining how, in an adaptive management framework, scientific research 

informs management of environmental problems such as hypoxia (and vice versa). 
26 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

Chesapeake Bay Program, and Puget Sound 

Partnership. Many of the case studies presented 

in Appendix II provide additional descriptions 

of regional governance structures. Given the 

exponential increase in the number of systems 

experiencing hypoxia (Diaz and Rosenberg 2008), 

it is critical that more states take actions to reduce 

nutrient transport into the coastal zone. 

As highlighted in this chapter, each of the 

various research efforts conducted by Federal 

agencies or funded extramurally by Federal 

agencies has focused on understanding a different 

aspect of the hypoxia issue (Figure 9). Studies 

have addressed approaches for reducing nutrients 

at their sources, what happens to nutrients during 

transit through the watershed, how nutrients affect 

hypoxia and related water quality concerns in the 

coastal zone, and, finally, how hypoxia impacts 

aquatic life and ecological services provided by 

coastal systems. Recipients of extramural funds 

have included state governments and academic 

organizations that have coordinated their research 

with Federal research programs (see Appendix I). 

Many Federal agencies contribute to research 

and management of hypoxia and nutrients. The 

primary agencies include NOAA, EPA, USGS, and 

USDA. NOAA has focused research funds and 

internal capabilities on monitoring and improving 

understanding of hypoxia and its impacts on 

commercially- and ecologically-important living 

resources in coastal waters. EPA bridges the 

continuum from freshwater ecosystems to estuaries 

and coastal waters and has focused resources on 

understanding and regulating nutrient inputs, such 

as those from wastewater treatment plants, as 

well as studying and modeling hypoxia in coastal 

waters. USGS provides critical data through the 

measurement and modeling of freshwater and 

nutrient delivery to coastal waters throughout 

the Nation. Finally, USDA is responsible for 

developing and implementing strategies to reduce 

nutrient inputs to coastal waters from agricultural 

lands and urban ecosystems, which is a major cause 

of eutrophication and hypoxia in many systems. 

Recent research accomplishments for these Federal 

agencies are highlighted in this chapter and in the 

place-based case studies in Appendix II. Appendix 

I provides details about programs in Federal 

Box 4. Adaptive Management Approach for Gulf of Mexico Hypoxic Zone

HABHRCA 1998 mandated an integrated scientific assessment of hypoxia in the northern Gulf of Mexico. The 

findings on how and why hypoxia forms in the Gulf informed the first Action Plan signed by Federal and state 

agencies in 2001. The final recommendation of the 2001 Action Plan called for an updated scientific assessment 

to be completed in five years which in turn would lead to an updated Action Plan. Following the release of the 2001 

Action Plan, the Task Force completed a series of reports, including A Science Strategy to Support Management 

Decisions in 2004 and The Management Action Review in 2006. A series of four state-of-science symposia were 

also completed in 2006. These symposia and reports fed into a comprehensive EPA Science Advisory Board 

Report. The findings from the reassessment directly informed the 2008 Action Plan, which was signed in June 

2008. 

The 2008 Action Plan recommends at least a 45% reduction in nitrogen and phosphorus flowing into the Gulf to 

reduce the size of the hypoxic zone to the 5000 km2

 target. Unfortunately, despite the positive intentions embodied 

in these various rounds of assessments and plans, the aerial extent of hypoxia in the Gulf has continued to grow, 

which indicates that an even broader, more forceful, perhaps regulatory, approach is needed.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 27

Federal Hypoxia and Watershed Science Research

agencies which address 

various aspects of hypoxia. 

Where appropriate, the 

Federal agency responsible 

for conducting or 

funding specific research 

accomplishments is 

parenthetically highlighted 

in blue text. 

3.1. Improving 

Understanding 

of Hypoxia in 

Coastal Waters

Identifying and 

characterizing the causes 

of hypoxia are critical 

for effective ecosystem 

management and depend 

heavily upon monitoring 

programs and the development of models. 

Differences in factors that cause hypoxia 

among systems, ranging from primarily 

nonpoint source nutrients in the northern 

Gulf of Mexico to wastewater treatment 

plant effluent in Narragansett Bay (Figure 

3), highlight one source of complexity in 

mitigating and controlling hypoxia in different 

coastal systems. The following sections 

highlight recent monitoring (Section 3.1.1) 

and modeling (Section 3.1.2) activities 

and advances in understanding of hypoxia 

characteristics and causes (Section 3.1.3). 

3.1.1. Monitoring Hypoxia 

Monitoring of dissolved oxygen in coastal 

waters is usually conducted as a component 

of research and water quality monitoring 

programs. Many such programs are conducted 

through partnerships involving one or more 

agencies of the Federal government, one or 

more states, and local government. EPA’s 

National Estuary Program (NEP) supports 

such partnerships around the country in order 

to implement environmental monitoring. As 

part of their respective missions, EPA and 

USGS conduct long-term assessments of 

Box 5. Adaptive Management Approach 

for Chesapeake Bay 

In 1983, following the 

conclusion of a 5-year EPA 

Chesapeake Bay Study 

and other water quality 

initiatives, Bay states and 

the Federal government 

agreed to reduce nitrogen 

inputs into the Bay through 

the first Chesapeake Bay 

Agreement. A Scientific and Technical Advisory Committee 

was formed at this time and released its first report in 1986. 

The scientific information and consensus in this report 

led to the Second Chesapeake Bay Agreement in 1987, 

calling for a basin-wide nutrient reduction strategy and more 

stringent nutrient reduction targets. Reevaluations in 1992 

and 1997 then led to the Chesapeake 2000 Agreement, 

which recommitted to goals of the prior agreements while 

outlining more specific strategies for achieving the targets. 

In support of the adaptive management process, the 

Chesapeake Bay Program recently agreed to a framework 

for a five-stage adaptive management model (Kaplan and 

Norton 2008). 

A recent assessment of water quality trends in rivers 

feeding the Bay showed significant improvements for 

nutrient loading for nitrogen (72%), total phosphorus (81%), 

and sediment (43%), indicating that management actions 

are having some effect in reducing nutrients and sediments 

(Langland et al. 2006). However, to date, the management 

of nutrient input in the Chesapeake Bay has not improved 

dissolved oxygen, although it has caused small-scale 

reversals in hypoxia (Diaz and Rosenburg 2008). 

Figure 9. Schematic describing general areas of hypoxia-related research. This 

illustration explains the organization of Chapter 3.
28 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

environmental and ecological conditions, including 

dissolved oxygen, within selected bays, estuaries, 

and other coastal waters. The Integrated Ocean 

Observing System (IOOS; NOAA), which seeks 

to integrate all ocean and coastal data within a 

national monitoring framework, does not currently 

include dissolved oxygen as one of its five high 

priority variables for synthesis. However, some 

of the regional ocean observing systems that 

contribute to IOOS collect dissolved oxygen data 

(Appendix I).

There is regionally focused monitoring of 

dissolved oxygen in the Chesapeake Bay (EPA, 

NOAA, USGS), Narragansett Bay (NOAA, EPA), 

Hood Canal, Lake Erie (NOAA), Long Island 

(EPA), and along the Oregon continental shelf 

(NOAA, National Science Foundation or NSF; see 

Figure 10 for examples). Most of the 27 National 

Estuarine Research Reserves (NOAA–state 

partnerships, recently summarized by Sanger et 

al. 2002) monitor dissolved oxygen through the 

System-Wide Monitoring Program (SWMP). 

Finally, routine monitoring of dissolved oxygen 

as part of juvenile salmonid surveys from Oregon 

to the Canadian border along the shelf began in 

2006 in order to monitor the upwelling dynamics 

that have caused periodic hypoxia off the coast of 

Oregon (NOAA).

Monitoring in the northern Gulf of Mexico, the 

largest hypoxic zone in the United States (Figure 

10d) and one of two hypoxic zones located in 

Federal waters (the other one is off the Oregon 

coast, see Appendix II) has received increasing 

attention in recent years. Since 1985, an annual 

shelf-wide survey has been conducted during 

July, when hypoxia is presumed to be most 

widespread. Although this has been funded as part 

of a competitive research program, the surveys 

have provided the principal metric for assessing 

progress toward the goal of a reduction in hypoxia 

outlined by the Gulf of Mexico/Mississippi River 

Watershed Nutrient Task Force (see Gulf of Mexico 

case study, Appendix II) and for validating hypoxia 

forecasts (NOAA). Other ship-based sampling 

of water quality (including dissolved oxygen) on 

the continental shelf and near major outlets of the 

Mississippi and Atchafalaya Rivers occurs annually 

and seasonally as a part of shelf-wide surveys and 

hypoxia-related research (NOAA, EPA). These 

surveys were designed to quantify key physical 

and biogeochemical processes influencing the 

development and persistence of hypoxia, and to 

support development of predictive models (NOAA, 

EPA). Seasonal field surveys using EPA’s offshore 

survey vessel and satellite ocean color remote 

sensing were conducted in 2003, 2006, and 2007 

to characterize the magnitude and variability in 

physical, biological, and chemical oceanographic 

conditions and processes along the northern Gulf 

continental shelf from the Mississippi River Delta 

to Texas (EPA). NOAA’s Gulf of Mexico Hypoxia 

Watch (http://ecowatch.ncddc.noaa.gov/hypoxia) 

has provided internet access to summer seasonal 

dissolved oxygen data collected through routine 

the Southeast Area Monitoring and Assessment 

Program (SEAMAP) groundfish monitoring 

cruises in June and July (NOAA). Several moored 

instrument arrays have also been deployed in the 

Gulf of Mexico hypoxic zone to obtain continuous 

records of dissolved oxygen. Efforts to improve 

and test the moored instruments are continuing 

(NOAA, Minerals Management Service). 

Box 6. Sound Science Leads to 

Significant Reductions in Hypoxia in 

Long Island Sound

Following progressive declines in water quality 

and increasing prevalence of hypoxia, the Long 

Island Sound Study (LISS) was formed in 1985 to 

guide the recovery of the Sound. The LISS released 

a Comprehensive Conservation Management Plan 

in 1994 that outlined 3-phases: 1) in 1990, freezing 

nitrogen loadings in critical areas to prevent worsening 

of hypoxia, 2) implementation of low-cost nitrogen 

reduction measures, and 3) reduction of nitrogen 

loads to target levels. In 1998, the LISS adopted a 

58% nitrogen reduction target by 2014 and in 2001, 

the EPA approved state total maximum daily loads 

(TMDL) plans to achieve this goal. By 2005, point 

source nitrogen loads had been reduced by 20% from 

the peak in the 

early 1990’s 

and the severity 

of hypoxia 

declined (see 

Long Island 

Case Study in 

Appendix II).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 29

Federal Hypoxia and Watershed Science Research

Recognizing the need to expand coastal 

monitoring in the northern Gulf of Mexico 

and move funding from a competitive research 

mechanism to an operational monitoring 

framework, NOAA convened a workshop in 

January 2007 entitled “Summit on Long-Term 

Monitoring of the Gulf of Mexico Hypoxic 

Zone: Developing the Implementation Plan for 

an Operational Observation System.” Three 

committees were formed as a result of the Summit 

(executive, technical, and stakeholder) and have 

worked to develop a monitoring implementation 

plan, which includes detailed designs and cost 

estimates. This plan was completed in December 

2008. Operational monitoring for the northern 

Gulf of Mexico is important for tracking progress 

in remediating hypoxia and support forecasts 

and other scientific research needed to inform 

management. Implementation of this plan is a 

priority.

Box 7. Hypoxia Advanced Warning 

Protects Drinking Water

Since 2006, when three out of four Cleveland 

water treatment plans were exposed to anoxic waters 

carrying increased loads of certain metals, NOAA 

deployed water quality monitoring sensors as part of 

its Real-time Coastal Observation Network (ReCON) 

near the plants’ water intakes. The ReCON sensors 

provided advanced warning of hypoxia in 2007, 

allowing the Cleveland Water Division to adjust their 

water treatment approach to maintain the safety of 

water supplies for 1.5 million people.

Real-time Coastal Observation Network (ReCON)

Figure 10. Hypoxia is most intensively monitored in the largest and most impacted coastal systems in the 

United States. Examples include: a) Long Island Sound, b) Chesapeake Bay, c) Lake Erie, and d) Northern Gulf 

of Mexico.

a) b)

c)

d)

Image: EcoCheck and Chesapeake Bay Program

Image: IFYLE Program

Image: CT DEP

Image: LUMCON, NOAA
30 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

3.1.2. Modeling and Forecasting Hypoxia

Environmental models can range from simple 

statistical equations to complex, computerintensive three-dimensional simulations that 

incorporate various aspects of physical, chemical, 

and biological processes in a coastal waterbody 

and its watershed. Models are essential tools for 

making scientific inferences when systems are 

too large or complex to conduct manipulative 

experiments. Weather forecast models are the 

most widely appreciated environmental models, 

but environmental models are also widely used for 

air quality forecasting and management, fisheries 

management, emergency management, and water 

quality management, among others. Models are 

particularly useful for understanding hypoxia 

because hypoxia reflects strongly coupled physicalchemical-biological processes. Computer intensive 

water quality models have been used for nearly 

three decades to predict the impact of nutrient 

management actions on specific water quality 

outcomes, including the extent and severity of 

hypoxia. 

Coupled watershed-water quality models have 

been a critical tool in the effort to manage nutrients, 

reduce hypoxia, and, more broadly, restore the 

health of the Chesapeake Bay ecosystem. The 

EPA Chesapeake Bay Program has funded water 

quality model development by the U.S. Army 

Corps of Engineers Waterways Experiment Station 

and others since 1987 and has relied heavily on 

the resulting models to guide nutrient reduction 

strategies throughout the Chesapeake Bay 

watershed (Koroncai et al. 2003; Cerco and Noel 

2004, 2005). Model results provide options to be 

analyzed in the course of determining a nutrient 

management strategy. A deliberative process based 

on model results is necessary because all models, 

even if very useful, are imperfect and subject to 

error (Koroncai et al. 2003).

While efforts to improve Chesapeake Bay 

modeling are ongoing, recent Federal modeling 

efforts have focused heavily on model development 

in the northern Gulf of Mexico hypoxic zone, 

which has followed a somewhat different 

trajectory. A variety of relatively simple models 

Table 5. Models developed since 2002 to forecast or simulate Gulf of Mexico hypoxia 

(adapted from Justic ́ et al. 2007).

Model Class Key Outputs Key Attributes 

Greene et 

al. (2009)

Statistical Substantial and sustained nitrogen 

and phosphorus reductions are 

required to reduce hypoxia. 

Indicated dependence of conclusions on 

model choice and input data and provides 

estimates of forecast uncertainty.

Justic ́ et 

al. (2002) 

Simulation Riverine nutrients play a major role in 

the development of hypoxia. 

Provides estimate of time series of oxygen 

at a single location. Includes mechanistic 

detail. 

Scavia et 

al. (2003, 

2004) 

Simulation Extensive hypoxia not common 

before mid-1970’s. A 40-45% 

reduction is nitrogen may be required 

to meet management goals.

Provides estimates of forecast uncertainty 

using a biophysical modeling scheme. 

Stow et al. 

(2005) 

Statistical Stratification is a predictor of hypoxia 

and the amount of stratification 

required to induce hypoxia has gone 

down (1982-2002). 

Uses statistical approach to characterize 

long-term change in hypoxia relative to 

stratification strength. 

Turner et 

al. (2005, 

2006) 

Statistical Hypoxic zone has only recently 

developed (1970’s or 1980’s) and 

nitrogen is the major driving factor 

controlling the size.

Incorporates spring nitrate, river 

discharge, and year factor to predict 

hypoxia

Hetland 

and 

DiMarco 

(2008) 

Simulation Biological processes controlling 

hypoxia vary from east to west. 

Hypoxia is formed in place, and not 

advected across shelf.

Uses 3-dimensional hydrodynamic model 

with simplified water quality model to 

explore implications of different controls 

on oxygen consumption for the spatial 

distribution of hypoxia. 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 31

Federal Hypoxia and Watershed Science Research

have been developed to forecast the response of 

hypoxia to various nutrient load scenarios. In 

addition, more complex models have been and 

are being developed to improve understanding 

of basic scientific questions (Table 5). Coupled 

hydrodynamic-water quality models have been 

developed for the northern Gulf but these models 

lack important mechanistic details, particularly in 

their representation of biogeochemical and other 

biological processes (Table 5). 

Despite being recently developed and still 

relatively basic, models have nonetheless been 

very influential in setting nutrient reduction targets 

for hypoxia in the northern Gulf of Mexico (U.S. 

EPA 2007, Justić et al. 2007; NOAA). Simple 

regression models relating hypoxia to either 

nutrient loading (Turner et al. 2006b; NOAA) 

or freshwater flow and nutrient concentration 

(Greene et al. 2009; EPA) have proven surprisingly 

predictive. The model by Turner et al. (2006b) 

has been used annually since it was published 

to forecast the expected extent of hypoxia in 

midsummer. A suite of regression models 

(Greene et al. 2009; EPA) explore how model 

selection may influence possible conclusions and 

applications. Both studies suggest that a decrease 

in nutrient loads from the Mississippi Atchafalaya 

River Basin (MARB) on the order 

of 45% will be sufficient to reduce 

the extent of hypoxia on the shelf to 

the goal (five-year average of 5,000 

km2

) established in the first Gulf 

Hypoxia Action Plan. Turner et al. 

(2006b) suggest that hypoxia was not 

present on the shelf prior to the mid 

1970s, whereas Greene et al. (2009) 

conclude that hypoxia likely occurred 

as early as the 1950s, but most likely 

was much less extensive and perhaps 

did not occur every year as it 

presently does.

Scavia et al. (2003, 2004; NOAA) 

employ a biophysical model to 

parameterize the physical regime on 

the northern Gulf of Mexico shelf 

and forecast hypoxia extent (Figure 

11). Scavia et al. (2003, 2004) and 

Greene et al. (2009) each provide models that 

forecast the extent of hypoxia as a function of 

nutrient inputs with quantified bounds of forecast 

uncertainty, a useful development for management 

applications. These essentially empirical models 

provide a scientific rationale for the 45% reduction 

in both nitrogen and phosphorus loading that has 

been suggested to be needed in order to achieve 

the hypoxia reduction target for the Gulf. They 

lack, however, explicit simulation of ecological 

processes that might be used to better address 

fundamental questions regarding ecological 

controls on the extent and intensity of hypoxia 

as well as the impacts of hypoxia. For these 

applications, process-oriented dynamic simulation 

models would be preferable. These models would 

be more similar to the coupled hydrodynamicwater quality models that have been developed for 

the Chesapeake Bay (Cerco and Noel 2004, 2005).

For simulation models, the Regional Ocean 

Model System (ROMS), a multi-purpose, 

multidisciplinary, open source oceanic modeling 

tool, is being adapted to Narragansett Bay and will 

be coupled with an ecological model to improve 

understanding of the conditions driving hypoxia 

in that system (NOAA). The ROMS model is 

also now functional for the Chesapeake Bay, and 

Figure 11. Ensemble forecasts of the response of hypoxia to changes in 

riverine nitrogen load. Loads are percent reduction from the 1980–1996 mean 

May–June total nitrogen loads. The grey shaded area, representing the ensemble 

forecast, contains all values from 1,000 simulations. The horizontal bar at 5,000 

km2 represents the Action Plan goal. The blue area represents the range of 

nitrogen load reductions needed to achieve that goal. Most of the Gulf of Mexico 

hypoxia models agree that an approximately 45% reduction in both nitrogen and 

phosphorus are required to reduce the size of the hypoxic zone to the goal set by 

the Mississippi River/Gulf of Mexico Watershed Nutrient Task Force (adapted from 

Scavia et al. 2003, 2004). Hypoxic Zone Area (km) 

N Load Reduction
32 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

a new project is focused on adding ecological 

and sediment components to predict impacts of 

climate and nutrients on hypoxia and the ecosystem 

(NOAA). The ROMS ecological hybrid model is 

also being adapted for the finer-scale resolution 

existing in the shallower, narrower Delaware 

Inland Bays which periodically experience fish 

kills due to severe diel hypoxic events (NOAA). 

A modified version of the ROMS model uses a 

number of oceanographic and meteorological 

variables to examine the effects of water column 

stratification and circulation on hypoxia in the 

northern Gulf of Mexico (Hetland and DiMarco 

2008, NOAA). Additionally, Justic ́ et al. (1996, 

2002; NOAA) developed another simulation 

model, a coupled biological-physical model to 

examine oxygen cycling dynamics in the core of 

the hypoxic zone. This model used a number of 

forcing functions including nitrate loads, monthly 

Mississippi River runoff, and oceanographic 

and meteorological conditions. It enabled the 

simulation of historical oxygen concentrations and 

the linking of Mississippi River nutrient loadings to 

eutrophication.

Models can also be used to assess estuarine 

system susceptibility to hypoxia as a result 

of nutrient enrichment. An initial version of 

a Nitrogen-Phytoplankton-Detritus-Oxygen 

(PDO) model is being developed to address 

estuarine susceptibility to nutrient enrichment, 

considering the effects of nutrient loading, flushing, 

stratification, denitrification, and temperature 

(NOAA). A preliminary PDO model is being 

tested on 87 estuaries and shows promise in 

predicting chlorophyll-a concentrations across 

a range of estuarine types. The model could be 

used to determine which estuaries, especially ones 

not currently impacted, are most susceptible to 

secondary effects of enrichment. This information 

could help drive preventative management actions.

Finally, as part of the International Field Years 

on Lake Erie (IFYLE, NOAA), an international 

government and academic partnership, a major 

effort has been underway since 2005 to model 

various aspects of the Lake Erie ecosystem with 

a special emphasis on understanding the causes 

and dynamics of hypoxia. In an effort to develop 

a modeling framework that could help synthesize 

the data collected during IFYLE, a new project will 

employ a number of modeling approaches (e.g., 

watershed, river hydrology, lake hydrodynamics, 

lower food web, spatially explicit higher food web, 

statistical) to help identify the causes of hypoxia in 

Lake Erie and its consequences for the Lake Erie 

food web (NOAA).

3.1.3. Identifying Causes and 

Characteristics of Hypoxia

Chapter 2 provides an overview of the general 

causes of hypoxia. In addition, Appendix II covers 

a series of specific case studies which provide 

additional detail about causes and characteristics 

of hypoxia in highlighted systems. In general, 

advances have been made in understanding the 

relationship between various nutrients and the size 

or extent of hypoxia. For instance, determining 

that phosphorus is a limiting nutrient for primary 

production on portions of the continental shelf 

in northern Gulf of Mexico waters led to a call 

for reduction in both nitrogen and phosphorus 

levels being transported down the Mississippi 

River (NOAA, EPA). In addition, there has been 

improved understanding of the influences that 

physical oceanographic variables (e.g., salinity 

and currents) have on hypoxia formation and 

characteristics.

Understanding what aspects of the physical 

system allow hypoxia to develop and tracking how 

it changes through time have been active areas of 

research for most systems that experience hypoxia. 

Additionally, hypoxic waters tend to remain near 

where they were formed, suggesting that currents 

do not move hypoxia across the shelf (NOAA). 

The structural features (horizontal and vertical 

characteristics) of hypoxia have been accurately 

reproduced using a combination of benthic 

respiration and hydrodynamic models. This has 

reaffirmed the observed spatial and temporal 

variability of the hypoxia, especially towards the 

end of the hypoxia season. Different processes 

regulate the formation of hypoxia in different 

regions of the hypoxic zone. Additionally, despite 

being disrupted by hurricanes (which serve to 

mix the water column and oxygenate the bottom 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 33

Federal Hypoxia and Watershed Science Research

layer), the hypoxic zone can be resilient, quickly 

reforming once the storm has passed (NOAA). 

The physical circulation of Narragansett Bay has 

been well studied through the use of strategically 

deployed shipboard and moored instruments. 

Recent results show that stratification is a major 

driver for hypoxia, with hypoxia happening most 

often in summer several days after a neap tide 

(NOAA). Meanwhile, efforts to determine the 

causes of hypoxia off the Oregon shelf (e.g., 

Chan et al. 2008) are being pursued after hypoxia 

and anoxia in waters less than 50 m deep caused 

massive mortality of benthic organisms (NOAA, 

NSF). Upwelling dynamics are important for 

many of the west coast systems experiencing 

hypoxia such as Yaquina Bay and Hood Canal (see 

Appendix II).

National assessments by a variety of Federal 

agencies and Federal-state partnerships, with the 

support of academic scientists, have revealed and 

characterized widespread nutrient pollution in 

estuarine waters (CENR 2000, 2003; NRC 2000; 

U.S. Commission on Ocean Policy 2004). The

EPA Water Quality Inventory reported that 17% 

of the estuarine waters assessed were impaired 

by low dissolved oxygen due to anthropogenic 

eutrophication (U.S. EPA 2002). EPA’s NEP 

and National Coastal Assessment Program and 

the NOAA’s National Centers for Coastal Ocean 

Science have been formally monitoring and 

assessing individual estuaries since the early 1990s 

and have broadly reported that estuarine water 

quality has been degraded by excess nutrients and 

eutrophication (U.S. EPA 2005, 2008; Bricker et al. 

1999, 2007).

The first National Estuarine Eutrophication 

Assessment (Bricker et al. 1999, NOAA), a 

survey of the extent, severity, types, probable 

causes, and future outlook of eutrophic symptoms, 

was conducted in the early 1990s. An update, 

examining the status of eutrophication in the 

early 2000s and the changes that have occurred 

since the early 1990s, was completed in 2007 

(Bricker et al. 2007). For both reports, data and 

information were collected for 141 estuaries and 

coastal waterbodies from scientists and resource 

managers from academia, state, and Federal 

agencies (i.e., USGS, EPA, and NOAA), as well 

as nongovernmental organizations. This national 

assessment emphasizes the need for a coordinated 

and integrated effort that balances management 

action, efficient monitoring to assess the 

effectiveness of the management, focused research, 

and a communication campaign aimed at engaging 

the broader public.

3.2. Quantifying and 

Modeling the Impacts of 

Hypoxia 

As discussed in Chapter 2, quantifying the 

impacts of hypoxia remains a critical information 

gap. The state-of-knowledge related to hypoxia 

impacts, as well as the research and management 

needs, were assessed in the NOAA-supported 

“Ecological Impacts of Hypoxia on Living 

Resources Workshop,” which was held in March 

2007. A peer-reviewed special issue of the Journal 

of Experimental Marine Biology and Ecology, 

which resulted from the 2007 workshop and 

contains the most up-to-date knowledge of hypoxia 

impacts, was published in 2009 (Lewitus et al. 

Figure 12. Trends in catch per unit effort for brown 2009). The major results from this workshop and shrimp in the northern Gulf of Mexico (modified from 

Downing et al. 1999).
34 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

other Federally funded research are presented 

below.

Quantifying the ecological impacts of hypoxia 

is essential for developing meaningful targets 

for hypoxia mitigation strategies (e.g., goals 

for areal extent or periodicity of hypoxia). A 

number of effects on living resources have 

been documented in both field and laboratory 

experiments. Many of these effects are dependent 

on both the temporal and spatial scale of hypoxic 

events and can be manifested through both direct 

and indirect impacts. Current research suggests 

that effects at both the population and individual 

levels are likely to be revealed not only through 

direct means, such as fish kills, but also through 

complex indirect, often sub-lethal mechanisms, 

such as reduced reproductive output and growth. 

However, separating the effects of hypoxia from 

other stressors that also negatively influence 

populations and individuals is extremely difficult. 

For example, trends in the catch per unit effort of 

brown shrimp in the northern Gulf of Mexico are 

consistent with impacts from hypoxia, habitat loss, 

overfishing, and economic factors (Figure 12). But 

the area of hypoxia may have a greater influence 

on annual landings (Figure 13). Models which 

relate experimental field and laboratory studies to 

population-level changes in fisheries and potential 

economic impacts are being developed for several 

systems including the Neuse/Pamlico River 

estuary, Lake Erie, Chesapeake Bay, Delaware 

Inland Bays, and northern Gulf of Mexico 

(NOAA). 

3.2.1. Mortality and Altered 

Distribution of Fauna

Faunal mortality (e.g., fish kills) has been 

documented in most coastal systems affected 

by hypoxia and is often a factor of the duration 

and extent of hypoxic conditions. Most of 

the species affected are invertebrates that are 

unable to move (e.g., clams) when dissolved 

oxygen becomes too low. This has been best 

documented in the Chesapeake Bay, where 

summer hypoxia typically causes mortality 

among immobile bottom-dwelling organisms 

(e.g., clams, mussels, and worms) in deep water 

(see Seitz et al. 2009). Similarly, mortality 

events in the northern Gulf of Mexico are 

typically limited to immobile benthos within 

the hypoxic zone, although mortality of mobile 

fauna has also been reported (see Rabalais et 

al. 2001). Elsewhere, the increasing frequency 

of transient hypoxic events in Puget Sound has 

resulted in large localized die-offs of fish and 

shellfish species, while die-offs of menhaden 

and other species have been increasing in 

frequency in the Neuse River, North Carolina 

and in Narragansett Bay, Rhode Island. These 

areas were also sites of benthic faunal die-offs, 

especially in Narragansett Bay where hypoxia 

has resulted in localized loss of blue mussel 

populations (Altieri and Witman 2006). 

Although it has been long known that mobile 

organisms, especially fish, avoid hypoxic waters, 

the extent and pattern of movements have only 

recently been documented. In most systems, 

including the Chesapeake Bay and the northern 

Gulf of Mexico, virtually all bottom-dwelling 

mobile species (e.g., Atlantic croaker, Craig 

and Crowder 2005), as well as some openwater species (e.g., bay anchovy, Taylor et al. 

2007) are absent in bottom waters of hypoxic 

areas, while in Lake Erie fish are typically not 

found beneath the thermocline where dissolved 

oxygen can be low (Ludsin et al. 2009). Within 

Figure 13. Relationship between annual landings of brown 

shrimp in the northern Gulf of Mexico and the size of the 

hypoxic zone (O’Connor and Whitall 2007).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 35

Federal Hypoxia and Watershed Science Research

Delaware’s coastal bays, juvenile weakfish avoid 

hypoxic conditions caused by diel oxygen cycling, 

resulting in the daily emigration of weakfish out of 

tidal tributaries and their preferred habitats (Tyler 

and Targett 2007). Movements of Atlantic croaker 

and shrimp in the Gulf of Mexico have produced 

a “halo effect” which describes the congregation 

of fish around the edge of the hypoxic zone (Craig 

and Crowder 2005, Craig et al. 2005). Changes 

in zooplankton distribution have also been 

observed in Lake Erie, the Gulf of Mexico, and 

the Chesapeake Bay, with changes in biomass size 

spectra detected in the latter two systems. There 

have also been anecdotal reports that commercial 

fishing has adapted to hypoxia-induced altered 

spatial distribution, possibly placing concentrated 

prey at risk of overfishing. 

As would be expected, an analysis of fishery 

landings in 22 ecosystems that experience 

seasonal hypoxia (> 40% of total bottom area 

affected) determined that pelagic species such as 

Clupeoid fish were more abundant than bottomdwelling species such as crustaceans. Systems 

experiencing increased nutrient loadings, but 

not hypoxia, experienced the opposite effect on 

species composition, with more bottom-dwelling 

crustaceans than pelagic fish (Breitburg et al. 

2008).

Hypoxia-induced population migrations likely 

reflect an effective loss of preferred habitat for 

some species (Figure 14). The congregation of 

Atlantic croaker and brown shrimp along the edge 

of the hypoxic zone in the Gulf of Mexico (the 

halo-effect) suggests a loss of preferred habitat. 

Further, white shrimp spend a critical portion of 

their life cycle within the Gulf of Mexico and 

can be excluded from optimal spawning habitat. 

Hypoxia in the Chesapeake Bay has reduced and 

fragmented habitat for endangered sturgeon, likely 

hampering the species recovery (Niklitschek 

and Secor 2005). In addition to exclusion from 

preferred physical habitat, migrational patterns 

of species have been altered both in the Gulf of 

Mexico (e.g., brown and white shrimp) and along 

the coast of New Jersey (e.g., blue fish, Garlo et al. 

1979). 

3.2.2. Changes in Food Web Structure 

and Physiology

An emerging, indirect impact of hypoxia is the 

alteration in predator-prey relationships and food 

web functions that often involve complex pathways 

through cascading effects. Shifts in diets can result 

in changes in the transfer of energy through the 

food chain. Hypoxia-induced shifts in diet have 

been documented in a number of systems and 

typically result in shifts from bottom-dwelling to 

pelagic food items (Baird and Ulanowicz 1989, 

Baird et al. 2004). Additionally, the availability 

of suitable prey can be limited for planktivorous 

fish (fish that eat plankton) during severe hypoxia, 

due to hypoxia-induced changes in plankton 

distribution and segregation from predators (Zhang 

et al. 2009). Conversely, it has been hypothesized 

that the altered spatial distribution of organisms can 

also increase predation by concentrating prey, such 

as along the edge of a hypoxic area. There can also 

be benefits to both prey and predators, but these are 

species dependent. For example, in Narragansett 

Bay, quahogs benefited from reduced predation 

pressure during moderate hypoxic conditions, 

whereas blue mussels suffered high mortality 

under similar conditions and thus received no 

benefit from reduced predation (Altieri 2008). 

Varying tolerance to hypoxia can also increase 

the abundance of certain predators. For example, 

hypoxia can lead to increased relative abundance of 

gelatinous zooplankton (jellyfish and comb jellies) 

which are more tolerant to low dissolved oxygen, 

Figure 14. Map of Gulf of Mexico with darker shaded 

areas indicating denser fish populations in the 1960s. 

Red line outlines current general configuration and geographic 

location of the hypoxic zone. Source: Kevin Craig, FSU.

Pre-Hypoxia Fish Catch (1961-1965)

1997 Dead zone: oxygen ≤ 2 mg/L 1997 Hypoxic zone: oxygen < 2 mg/L
36 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

which in turn leads to increased predation on fish 

larvae. The overall effects of hypoxia on food web 

structure have only recently begun to be quantified, 

but appear to be both species- and system-specific. 

Sustained, long-term hypoxia can ultimately lead to 

a total shift in food web structure, which has been 

observed in several systems (Rabalais et al. 2001, 

Baird et al. 2004). 

Researchers are increasingly examining sublethal physiological, reproductive, and bioenergetic 

impacts of hypoxia. A reported effect of hypoxia 

in commercially- and recreationally-relevant 

species is growth reduction. In the Gulf of 

Mexico, hypoxia has been linked to reductions 

in brown shrimp lipid content as well as size. In 

laboratory analyses, striped bass and menhaden 

growth were reduced, while field examinations 

have found reduced growth in both juvenile 

summer flounder and weakfish. Reproductive 

effects include alterations to reproductive organs, 

reduced production of offspring, and lowered 

rates of offspring survival. Atlantic croaker have 

also exhibited altered endocrine function and 

suppressed growth of ovaries and testes under 

similar conditions. Reduced egg production 

attributed to the effects of hypoxia has been found 

in Atlantic croaker, grass shrimp, and naked 

gobies in the Chesapeake Bay and Gulf of Mexico 

estuaries (Thomas et al. 2007). Further, egg 

survival can be reduced when eggs spawned within 

the water column sink into hypoxic water, as has 

been observed with bay anchovy and weakfish in 

the Chesapeake Bay (Breitburg 2002). Finally, a 

number of other sublethal or indirect physiological 

effects of hypoxia have also been documented 

including immune suppression in oysters 

(Anderson et al. 1998) and reduced consumption 

and respiration in fish and shellfish. 

3.3. Monitoring and 

Modeling Nutrient Flux in 

U.S. River Systems

Monitoring streamflow and nutrient fluxes in 

river systems that feed coastal estuaries is essential 

to understanding and predicting coastal hypoxia. 

Furthermore, knowledge of the sources of nutrients 

ultimately delivered to the coastal zone and 

knowledge of processes that reduce nutrient loads 

during transit are required for the development 

of effective management strategies for reducing 

coastal hypoxia. It is not economically feasible 

to monitor all the sources and fluxes of nutrients 

in all rivers and streams in the United States. 

However, models using monitoring data from 

targeted watersheds, representative in terms of their 

climate, geography, land use, and management 

measures, can be extremely valuable tools. These 

models can identify the geographic areas with the 

highest nutrient contributions, the human activities 

that contribute the most nutrients, the ecosystems 

that reduce nutrient fluxes, and potentially the 

management measures that are most effective at 

mitigating nutrient fluxes. 

3.3.1. Monitoring Nutrient Sources and 

Fluxes to Coastal Systems

There are two major components of riverine 

monitoring in the United States. The first 

component is monitoring delivery of streamflow 

and nutrient fluxes to coastal environments. This 

monitoring requires sufficient temporal resolution 

to enable development of cause and effect linkages 

between the timing of nutrient fluxes and the 

development of hypoxia. The second component 

comprises monitoring of inland watersheds. This 

monitoring happens in watersheds of various scales 

and supports modeling applications that define the 

spatial distribution of the sources of nutrients and 

the human activities that affect those fluxes. 

The USGS is the primary agency monitoring 

streamflow, nutrients, and other water quality 

constituents in rivers and streams throughout the 

United States. Other agencies rely on these data 

to determine effective conservation measures 

to protect downstream resources. Additional 

monitoring is conducted by state governments 

through water quality compliance programs under 

EPA oversight. Although limited by the objective 

and design, more and more of these data are being 

integrated into regional and national monitoring 

efforts.

An important element of the design of programs 

monitoring nutrient delivery to coastal systems 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 37

Federal Hypoxia and Watershed Science Research

is the availability of continuous streamflow 

records and water quality measurements taken 

with sufficient frequency to enable accurate 

estimation of nutrients fluxes (mass per unit 

time) with adequate temporal resolution. The 

U.S. Commission on Ocean Policy (2004) cited 

a critical loss of USGS stream gauging capacity 

due to funding constraints, which has limited the 

ability to monitor water and other constituents 

entering our coasts. Most monitoring programs are 

designed to measure the concentration of nutrients 

at the time of sampling, and measurements are 

only taken a few times each year. However, flux 

estimates are essential to evaluating the causal 

relationship between nutrient delivery and hypoxia 

and to evaluate trends, including the performance 

of management actions. 

The USGS National Stream Quality Accounting 

Network was redesigned in 2007 as a national 

coastal monitoring network with the primary 

goal of measuring delivery of streamflow and the 

associated fluxes of nutrients and selected other 

chemical constituents to coastal environments. 

The redesign maximizes existing resources and 

ongoing monitoring programs (such as the USGS 

National Water Quality Assessment Program 

and state monitoring programs). In 2008, five 

additional stations were added to this national 

coastal monitoring network as a result of the initial 

steps of implementation of the National Monitoring 

Network of the Ocean Action Plan, thereby 

increasing the number of large coastal rivers 

being monitored from 13 to 18. These 18 stations 

were selected because the rivers they monitor 

contribute the greatest percent of streamflow and 

nutrient fluxes to coastal environments. Seventeen 

stations are in the conterminous United States; the 

other is on the Yukon River in Alaska. Together, 

these stations measure more than 80% of the total 

discharge of streamflow, nitrogen, phosphorus, 

and suspended sediment to U.S. coastal waters 

(USGS). Samples are collected at most stations 

twelve times each year to enable accurate annual 

flux estimates for most constituents measured. 

Increased frequency of measurements is required 

to estimate seasonal or monthly fluxes with greater 

certainty and also to capture episodic events. This 

monitoring network does not address delivery of 

nutrients by smaller rivers to many local coastal 

ecosystems affected by hypoxia.

Monitoring of inland watersheds is conducted 

by a diverse group of local programs. However, as 

0

100

200

300

400

500

600

700

19791980198119821983198419851986198719881989199019911992199319941995199619971998199920002001200220032004200520062007

Avg. 79-07

2008

Year

Dissolved Nitrite plus Nitrate Flux as N,

in Thousands of Metric Tons

June

May

April

Figure 2. Estimated April, May, and June dissolved nitrite plus nitrate flux as N to the Gulf of Mexico for 1979 

through 2008. Maximum, minimum, and average fluxes are determined for the period 1979 through 2007. 

*Note that 2008 fluxes are preliminary as they are based on provisional data.

*

Maximum

Average

Minimum

Figure 15. Estimated nitrate delivery to the Gulf of Mexico for April, May, and June 

1979 - 2008. Maximum, minimum, and average fluxes are determined through 2007.

*Note that the 2008 deliveries are preliminary as they are based on provisional data. 

Source: Brent Aulenbach, USGS, http://toxics.usgs.gov/hypoxia/mississippi/oct_jun/graphics.

html
38 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

indicated above, the design limits their applicability 

to coastal assessments. USGS also monitors inland 

watersheds in selected major river systems that 

drain to the coast, using the same sampling design 

suitable for estimating annual nutrient fluxes. This 

monitoring is conducted in the MARB and in the 

Chesapeake Bay drainages. These data also are 

used to develop watershed models described in the 

following section of this report.

Within the MARB, measurements are made at 

19 inland stations. The delivery of streamflow 

and nutrients from the Mississippi River basin to 

the Gulf of Mexico for the first nine months of the 

water year (October through June) is reported each 

year in July to enable Gulf scientists to analyze and 

forecast the size of the hypoxic zone in the northern 

Gulf of Mexico (Figure 10b). The hypoxic zone is 

estimated each year in late summer. In addition, a 

summary of nutrient loads for all Mississippi River 

stations for the period of record through 2006 is 

available on the Internet (http://toxics.usgs.gov/

hypoxia/mississippi/nutrient_flux_yield_est.html). 

This dataset is updated annually (Figure 15). 

3.3.2. Modeling Nutrient Sources, Fate, 

and Transport

Watershed and nutrient transport, yield, and 

flux modeling efforts are being undertaken (EPA, 

NOAA, USDA, USGS) to identify and manage the 

most significant nutrient sources within watersheds 

draining to coastal areas experiencing hypoxia. 

These modeling efforts include the SPAtially 

Referenced Regressions On Watershed Attributes 

(SPARROW) Model (http://water.usgs.gov/nawqa/

sparrow/), the Soil and Water Assessment Tool 

(SWAT) Model (http://www.brc.tamus.edu/swat/), 

and the Regional Nutrient Management Model 

(ReNuMa, Hong and Swaney 2007; http://www.

eeb.cornell.edu/biogeo/nanc/usda/renuma.htm). 

The SPARROW model (Box 8) is a hybrid 

mechanistic/empirical, basin-scale simulation 

model developed by the USGS (Smith et al. 1997). 

It was developed to cover the entire conterminous 

United States. Since then, applications have 

been developed for watersheds of a wide range 

of scales, with data input refinements appropriate 

for the specific scale of application. It has been 

Box 8. Application of SPARROW for Reducing Nutrients to the Gulf of Mexico

An improved SPARROW model published in 2008 (Alexander et al. 2008, USGS) found that much of the 

nitrogen and phosphorus delivered to the Gulf originates from certain regions and watersheds of the Mississippi 

River Basin, including many watersheds in the Central Mississippi and Ohio, which contribute more than 50% of 

the nutrients despite accounting for less than 30% of the total drainage area (see inset). The study reveals new 

details about sources of phosphorus, indicating that animal manure on pasture and range lands contributes nearly 

as much phosphorus as cultivated crops, 37% versus 43%, respectively. The study reports that 66% of nitrogen 

originates primarily from cultivated crops, mostly corn and soybean, with animal grazing and manure contributing 

only about 5%. Atmospheric contributions also are important, accounting for 16% of nitrogen. These findings 

influenced the 2008 decision by the Mississippi River/Gulf of Mexico Watershed Nutrient Task Force to call for 

reductions in phosphorus, in addition to nitrogen, in an effort to control Gulf hypoxia.

Percentage of stream 

nutrient load delivered 

to the Gulf of Mexico: 

(a): total nitrogen; 

(b) total phosphorus. 

(Alexander et al. 2008).

a) total nitrogen b) total phosphorus
Scientific Assessment of Hypoxia in U.S. Coastal Waters 39

Federal Hypoxia and Watershed Science Research

used to estimate nutrient loads and concentrations 

in streams and to determine the proportion of 

stream loads that are derived from major sources 

of nutrients, including land use, chemical use, and 

human activities (e.g., agriculture, atmospheric 

deposition, human wastes). The model accounts 

for the effects of climate, topography, soils, and 

the effects of aquatic ecosystems to determine 

nutrient transport in watersheds. Formal estimates 

of uncertainties in the stream nutrient loads and 

source contributions are also reported. The model 

has been applied to small and very large watersheds 

in the United States and internationally to assess 

nutrient sources and loads to the Mississippi River 

basin (Alexander et al. 2000, 2008), New England 

watersheds (Moore et al. 2004), the Chesapeake 

Bay watershed (Preston and Brakebill 1999), 

New Zealand river basins (Alexander et al. 2002; 

Elliott et al. 2005), and North Carolina coastal 

watersheds (McMahon et al. 2003). Many of these 

applications have demonstrated the particular 

utility of the model for quantifying the longdistance transport and delivery of nutrients to 

sensitive downstream locations such as estuaries. 

Federal and state environmental managers have 

used the SPARROW model to assess nutrient 

sources in streams, including its use for targeting 

nutrient reduction strategies in the Chesapeake Bay 

watershed (Preston and Brakebill, 1999) and in 

waters of the State of Kansas (Kansas Department 

of Health and Environment, 2004), and for 

developing total maximum daily loads (TMDLs) 

in the Connecticut River basin (NEIWPCC, 2004). 

Regional nutrient models are currently under 

development in selected regions with the goal of 

refining the national SPARROW model as part 

of the USGS National Water Quality Assessment 

(NAWQA) Program.

The SWAT model was developed by the USDA

Agricultural Research Service (ARS; Neitsch et 

al. 2004; Arnold et al. 1998). It is a physically 

based, deterministic, continuous, watershed 

simulation model. It predicts water, sediment, 

nutrient, and pesticide yields using spatial data on 

topography, soils, land cover, land management, 

and weather. The SWAT model has been applied 

in the Mississippi River basin, including for large 

watershed-scale applications (Arnold et al. 1999; 

Anand et al. 2007), to evaluate agricultural nutrient 

reduction strategies (Santhi et al. 2001; Vache 

et al. 2002; Hu et al. 2007), address tile-drained 

Box 9. EPA Works Closely With States to Develop and Adopt Nutrient 

Criteria

• Direct assistance to states close to adopting criteria, particularly permitting implementation questions. 

In this regard, EPA’s Office of Science and Technology (OST) in the Office of Water works to 

develop tools to help states calculate the economic and ecological benefits of adopting water quality 

standards. OST has provided scientific peer review of proposed water quality standards packages 

for Vermont and draft nutrient criteria for Colorado. A cooperative assistance grant from EPA’s Gulf of 

Mexico Program to the Mississippi Department of Environmental Quality is assisting MS in all aspects 

of nutrient criteria development. MS will then lead the other Gulf of Mexico states in nutrient criteria 

setting for their own states through the Gulf of Mexico Alliance initiative. 

• Building capacity of States gathering and analyzing data. Over the past three years, OST has 

provided $2.5 million to support state nutrient criteria work. In 2008, EPA is analyzing nine nutrient 

data sets that will be used for nutrient criteria. EPA OST also developed a number of webcasts that 

provided expert technical guidance on nutrient criteria issues, with examples from states that have 

successfully developed nutrient criteria. 

• Building a science-based foundation for developing new Clean Water Act water quality criteria for 

estuaries, wetlands and Large Rivers: OST published a wetlands criteria technical guidance manual, 

developed case studies for two estuarine criteria efforts (Yaquina Bay, Oregon and Pensacola Bay, 

Florida) in collaboration with EPA’s Office of Research and Development, and are supporting four 

states (Maine, New Hampshire, Florida, and California) who are making progress on estuarine 

criteria. OST is also supporting nutrient criteria development efforts on several large rivers: the Big 

Sioux (South Dakota), the Missouri River, the Red River, and the Ohio River.
40 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

cropland (Du et al. 2006; Green et al. 2006), assess 

the impacts of climate change on nutrient export 

(Jha et al. 2006), and predict stream flow processes 

of a forested watershed in coastal South Carolina 

(Amatya et al. 2008).

A study comparing SWAT and a statistical 

approach based on SPARROW in the United 

Kingdom (Grizzetti et al. 2005) suggested using 

SPARROW as a screening tool for identifying 

sources, and SWAT for testing management 

practice scenarios, but found that both models 

were useful for estimating nitrogen loading in 

aquatic environments. Similarly, ARS and the 

NRCS of USDA have developed a system of 

computer models, the Agricultural Non-Point 

Source Pollution Model, to predict nonpoint source 

pollutant loadings in agricultural watersheds. This 

model contains a continuous simulation surface 

runoff model designed to assist in developing 

BMPs and TMDLs, as well as risk and cost/benefit 

analyses.

The ReNuMA model is a watershed model 

that enables the examination of various scenarios 

for reducing nitrogen losses from the landscape 

(EPA). Components of the model incorporate 

biogeochemical complexities and the impact 

of varying management practices on reducing 

nutrient loads. Continual development of the 

model has included an improved ability to 

incorporate atmospheric deposition and improve 

characterization of on-field nutrient management 

techniques to allow for more accurate simulation of 

varying management scenarios (NOAA).

3.4. Assessing, Managing, 

and Reducing Nutrient 

Inputs to Coastal 

Ecosystems 

This section discusses tools or management 

measures that are being studied and/or used to 

control or reduce nutrient delivery to coastal 

ecosystems. Nutrient fluxes to coastal ecosystems 

can primarily be reduced in two ways: (1) reducing 

nutrient inputs to rivers and streams, including 

losses of nutrients from farmlands and loads 

from point sources, urban and suburban nonpoint 

sources, and atmospheric deposition; and (2) 

restoring and enhancing natural denitrification 

and nutrient retention processes via restoration of 

riverine and coastal wetlands and in some areas, 

diversions of stream waters to coastal wetlands. 

3.4.1. Reducing Nutrient Inputs to Rivers 

and Streams

3.4.1.1. Establishing Nutrient Criteria

The Clean Water Act directs states and tribes 

to designate uses for their waters and adopt water 

quality criteria to protect those uses. Numeric 

nutrient standards are an important component 

to protecting water quality from excessive algal 

blooms and hypoxia because they drive water 

quality assessments and watershed management, 

facilitate development of TMDLs, provide 

quantitative targets to support nutrient trading 

programs, facilitate writing protective National 

Pollutant Discharge Elimination System permits, 

provide increased effectiveness in evaluating 

success of nutrient runoff minimization programs, 

and provide objective water quality baselines 

against which to measure environmental progress. 

Nutrient criteria benefit not only the local waters 

in which actions are focused, but also the receiving 

coastal waters. EPA’s Office of Science and 

Technology (OST) in the Office of Water (OW) is 

providing both technical and financial assistance 

to states to help them develop and adopt numeric 

nutrient standards (Box 9). 

Figure 16. Percent of the United States drained by 

artificial means such as tile drains (Jaynes and James 

2007).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 41

Federal Hypoxia and Watershed Science Research

from many local, state, and Federal agencies, 

including EPA and USGS. The mission of the 

ADMS Task Force is to reduce the loss of nitrogen 

and phosphorus from agricultural lands through 

drainage water management. The Task Force 

focuses on an eight-state region—comprised of 

Minnesota, Wisconsin, Iowa, Missouri, Illinois, 

Michigan, Indiana, and Ohio—that contains more 

than 50 million acres of surface- and subsurfacedrained cropland. The Task Force works with 

farmers, contractors, and agricultural advisors to: 

1) implement improved agricultural surface and 

subsurface drainage in both new and retrofitted 

systems; 2) reduce nitrate loads in drain outflow, 

a major source of poor stream water quality and 

hypoxia in the northern Gulf of Mexico; and 3) 

improve the efficiency of production and economic 

returns through managed surface and subsurface 

agricultural drainage. Implementation of managed 

drainage practices (NRCS Practice 554) in the 

Midwest began in 2004. Using demonstration 

sites, the Task Force educates local sponsors 

and farmers and works with them to implement 

managed drainage on their own land (http://

3.4.1.2. Tools and Management Strategy 

Development for Reducing Nutrient Loadings

Reducing nutrient loadings to streams and rivers 

surrounding and downstream from agricultural 

lands has been an active area of research for 

USDA. The re-engineering of the Midwest over 

the past 50 years with tile drainage systems that 

allow farmers to control subsurface water levels 

has benefitted U.S. agriculture through increased 

yields, but has negatively affected water quality by 

speeding water and its solutes—such as nitrogen, 

phosphorus, pesticides, and sediment—into streams 

and rivers without allowing natural elimination 

processes to occur (Jaynes and James 2007) (Figure 

16). As a result, USDA has made significant 

investments in conservation programs that remove 

marginal land from production, conservation 

improvements in working lands that reduce erosion 

and control nutrients, and the establishment of 

wetlands. In addition, USDA has worked with 

farmers and ranchers to encourage the use of 

buffer strips and improved tillage practices that are 

designed to prevent water quality impairments. 

Since nutrients often leave agricultural fields 

through drainage systems (e.g., tile drains, ditches), 

significant research by the USDA has focused on 

fine-tuning both surface and subsurface drainage 

applications (Box 10). In the Chesapeake Bay 

watershed, it has been estimated that nitrogen 

losses could be reduced by 40% by lowering 

the water table during planting and harvesting. 

Other modified surface drainage systems have the 

potential to reduce phosphorus by 30-50%, and 

nitrate and ammonium by 22-64%. In the Gulf of 

Mexico watershed, researchers have discovered 

that planting cool-season perennial forages such as 

alfalfa and grass directly over subsurface tile drains 

removes nitrate from the water table. Other options 

being explored include deep chiseling and the 

use of wood chips in drainage ditches to promote 

denitrification. 

Additionally, in 2003, NRCS and ARS (USDA) 

formed the Agricultural Drainage Management 

Systems (ADMS) Task Force, in concert with 

university research and extension personnel. The 

task force has since expanded to include scientists 

Box 10. Soil Drainage Research in 

Ohio

Scientists at USDA ARS’ Soil Drainage Research 

Unit in Columbus, Ohio, have developed an innovative 

agricultural water management system called a 

Wetland Reservoir Subirrigation System (WRSIS), 

comprised of a wetland and a water storage reservoir 

linked to a network of subsurface pipes used at 

different times to either drain or irrigate crops through 

the root zone. Runoff and subsurface drainage are 

collected from cropland into a constructed wetland. 

Natural processes in the wetland treat the water 

by removing some of the nutrients, pesticides, and 

sediment. The water is then routed to a storage 

reservoir and held until needed to subirrigate the 

crops during dry parts of the growing season. The 

storage reservoir also provides a further opportunity 

for sediment and adsorbed nutrients to settle out 

of the water. Most of the time, a WRSIS operates 

as a closed loop, thus restricting offsite water 

release. Benefits of these systems include: (1) 

enhanced crop yields; (2) reduced offsite release of 

nutrients, pesticides, and sediment; (3) increased 

wetland vegetation and wildlife habitat; (4) carbon 

sequestration in soil; and (5) the potential to decrease 

flooding downstream (http://www.ars.usda.gov/

Research/docs.htm?docid=14999).
42 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

extension.osu.edu/~usdasdru/ADMS/ADMSindex.

htm).

USDA has invested in developing a variety 

of strategies and technologies for more effective 

management of fertilizer applications. USDA 

developed the Nitrate Leaching and Economic 

Analysis Package model to evaluate the sensitivity 

of different regions to nitrate loss. USDA ARS 

developed the Phosphorus Index, an assessment 

tool that has been adopted by USDA NRCS, EPA, 

and various state agencies as the basis for their 

comprehensive phosphorus management plans. 

Adoption of this technology has been estimated to 

reduce annual phosphorus loadings in water by 56 

million pounds and sediment by 2.1 billion pounds. 

Economic benefits to society have been estimated 

at greater than $600 million dollars per year.

Considerable research has also focused on 

developing sensors to detect the water and 

nitrogen status of crops, which allows growers 

to target fertilizer and water applications to 

specific crop needs. By reducing unnecessary 

fertilizer applications, this approach is also more 

economical. The sensors, some of which have 

been developed through the Small Business 

Innovation Research Program grants to private 

industry, can be either ground-based or airborne. 

Ground-based sensors can be mounted on 

central pivot or other automatic 

irrigation systems. Researchers 

are also exploring how to reduce 

nitrogen and phosphorus release 

from fertilizers. The benefits 

of crop rotation, specifically the 

planting of soy before corn, are 

being used to justify applying 

less chemical fertilizer to corn 

since planting soybeans builds up 

a nitrogen credit. Farmers can 

save up to $30 per hectare with 

this approach. Finally, cover 

crops are a proven technology for 

the eastern and southern states, 

but are still being researched 

and introduced to Midwest 

farmers. Cover crops (Box 11) 

may be the best technology for 

simultaneously reducing nitrogen, 

phosphorus, and sediment from row crops. Further, 

USDA’s Conservation Reserve Program (CRP) 

is a voluntary program available to agricultural 

producers that protects environmentally sensitive 

land through planting of resource-conserving, longterm vegetative covers (Box 12).

Based on a rich dataset of observations and 

an improved, process-based simulation model 

(called the Root Zone Water Quality Model or 

RZWQM), ARS scientists have summarized and 

quantified the effects of management on nitrogen 

losses to surface waters through a series of papers 

published as a special issue of the scientific 

journal Geoderma (Ahuja and Hatfield 2007). 

Both water and nitrogen losses from tile-drained 

agricultural systems in the Midwest are addressed, 

as influenced by a variety of management practices. 

This special issue is a key resource for future 

efforts to control the magnitude and extent of the 

hypoxic zone in the Gulf of Mexico by reducing 

nitrogen loadings from tile-drained agriculture in 

the Mississippi River basin. Also, USDA’s Forest 

Service is developing practices to improve the 

capacity of nutrient-enriched watersheds to reduce 

nutrient loads in surface water and groundwater 

before they enter coastal waterbodies. For 

example, the creation of “hot spots,” places in a 

Figure 17. 2007 Map of CEAP projects, many of which are focused on the 

Mississippi River Watershed (http://www.nrcs.usda.gov/technical/nri/ceap/).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 43

Federal Hypoxia and Watershed Science Research

ARS completed development of the Sustaining 

the Earth’s Watersheds Through Research, Data 

Analysis, and Synthesis (STEWARDS) database—

an agency-supported repository for CEAP 

datasets collected as part of ARS’ Benchmark 

Watershed Research Network (available at http://

arsagsoftware.ars.usda.gov/stewards/).

3.4.2. Restoring and Enhancing Natural 

Nutrient Retention Processes to Reduce 

Pollution of Aquatic Environments 

Nutrient fluxes to coastal ecosystems can be 

reduced when nutrients already in stream systems 

are removed by natural processes that occur in 

riverine wetlands, certain types of reaches of 

watershed where denitrification could be enhanced, 

was shown to be an effective way to reduce the 

amount of nitrogen leaving urban watersheds 

(Strosneider et al. 2007, Pouyat et al. 2007), 

resulting in reduced nutrient loading of coastal 

waters.

In late 2002, the Office of Management 

and Budget asked NRCS (USDA) to quantify 

the benefits of Farm Bill-funded conservation 

programs. In 2003, the Conservation Effects 

Assessment Project (CEAP) (Figure 17, Box 11) 

was initiated by NRCS along with other USDA

agencies (ARS; Cooperative State Research, 

Education, and Extension Service or CSREES; 

and FSA) to improve scientific understanding 

of the effects of conservation practices at the 

watershed scale, and to estimate conservation 

effects for reporting at regional and national scales. 

The results are being used to manage agricultural 

landscapes for environmental quality. CEAP 

has grown into a USDA-led multi-agency, multiresource effort (Maresch et al. 2008). Duriancik 

et al. (2008) provide a detailed description of 

the approach of CEAP, and of accomplishments 

during its first five years. Specific details of ARS 

research accomplishments during the first five 

years of CEAP are collected in a special issue of 

the Journal of Soil and Water Conservation (2008). 

Box 11. Monitoring Winter Cover Crop Performance from Space

Planting winter cover crops is seen as an important management practice for reducing agricultural nutrient flows 

into the Chesapeake Bay and improving ecosystem health. The State of Maryland doubled its budget for its cover 

crops cost share program from $9 million to $18 million in 2008. This was enough for farmers to plant 500,000 

acres of cover crops after the fall 2008 harvest. USDA scientists at the Beltsville Agricultural Research Center 

have formed a strong partnership with the Maryland Department of Agriculture (MDA) for the evaluation of winter 

cover crop performance on the Eastern Shore of Maryland which is 

closely linked to the Bay. The evaluation uses a unique combination of 

remotely sensed data and program implementation information such as 

field location, planting date, cover crop type, and planting method, all 

supplied by participant farmers during program enrollment. Based on 

this information, detailed evaluation of cover crop program performance 

for growth and nutrient uptake can be obtained for all enrolled cropland 

fields within a region based on analysis of satellite images. This 

powerful new approach has led to improvements in the operation of the 

MDA program for cover crops. It has also demonstrated how satellite 

data can be used routinely to implement and monitor this important state 

conservation program. There are plans to jointly develop an operational 

cover crop implementation and monitoring tool based on technologies 

developed by this collaboration. This research effort is part of the 

Choptank River Watershed CEAP project.

Photo: Ben Longstaff, www.eco-check.org

Box 12. USDA Conservation 

Research Program Benefits in the 

Mississippi River Basin

In the Mississippi River Basin, the CRP presence is 

estimated to confer the following benefits annually:

• Reduced nitrogen runoff: 295 million pounds

• Reduced phosphorus runoff: 66 million pounds

• Reduced sedimentation: 100 million tons

• Protected/restored wetlands: 1.2 million acres

• Carbon dioxide sequestered: 12 million metric tons

• Enhanced wildlife habitat
44 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 3

river systems, and coastal/distributary wetlands. 

Existing and proposed freshwater diversions of the 

Mississippi River into the estuaries of southeastern 

Louisiana to mitigate land loss (from many factors 

including subsidence, salinity intrusion, etc.) have 

the ancillary benefit of removing nutrients.

The USGS SPARROW model was used 

to demonstrate that stream channel geometry 

can affect nitrogen removal in streams in the 

Mississippi River basin (Alexander et al. 2000). 

Small streams were found to have a significantly 

higher nitrogen removal rate, while larger 

streams acted more like conveyors, transporting 

the nitrogen load downstream. Therefore, the 

proximity of nitrogen inputs to larger streams is an 

important consideration for management actions 

because it influences whether the nitrogen in a 

stream will be carried to the Gulf of Mexico or 

removed.

The Riparian Ecosystem Management Model 

(REMM) simulates hydrology, nutrient dynamics, 

and plant growth in land areas between the edge 

of fields and a waterbody. REMM output allows 

designers to develop buffer systems to help control 

nonpoint source pollution (USDA). Analysis of the 

optimal composition of riparian buffers for nutrient 

removal has led to various design criteria, including 

the recommendation that trees or forests be part 

of the buffer, and analysis of the effectiveness of 

various grass species as alternatives. The grass 

analysis determined that all grasses except timothy 

were beneficial for nutrient removal (USDA). 

Some of the natural processes that reduce 

nutrient fluxes to receiving waters include: 1) 

restoration of riverine wetlands by the U.S. Fish 

and Wildlife Service (USFWS) and USACE, 

2) management of river flows to increase 

conditions conducive to increased nutrient 

reductions, such as lock and dam management 

on the upper Mississippi River, and 3) coastal 

diversions onto the Mississippi River delta 

at projects like the Caernarvon Freshwater 

Diversion Project. Similarly, flow management 

on the Mississippi River that diverts 30% of flow 

down the Atchafalaya River provides increased 

opportunity for nutrient removal in extensive 

distributary wetlands in the lower reaches of that 

river. USDA created more than 12.1 million acres 

of new wetlands in 2005 and 2006 as a result of 

research showing that water leaving a wetland 

had only a fraction of the nutrients (18%) than in 

the subsurface water entering the wetlands from 

agricultural fields. The wetlands program within 

USDA CRP was augmented by the 2008 Food, 

Conservation, and Energy Act, with a specific 

emphasis on encouraging producers to construct 

wetlands to remove nitrogen before it enters 

streams.

The strategic integration of perennials into 

agro-ecosystems provides greater benefits than 

their spatial extent suggest (Schulte et al. 2006; 

USDA Forest Service). Current research at the 

field, watershed, and landscape scales in the upper 

Mississippi River basin is focused on several 

components that contribute to the mitigation 

of nutrient loading to the Mississippi River. 

Researchers have employed simulation models to 

extrapolate results from small-scale studies over 

broad scales. Also, research is being conducted on 

the funding and social mechanisms needed to work 

with private landowners because, to be successful, 

the research must be participatory. The USDA

Forest Service’s Center for Bottomland Hardwood 

Research in Mississippi is a major partner in the 

effort to restore agricultural lands to bottomland 

hardwood ecosystems in the Mississippi Valley. 

An important part of the program is developing and 

delivering technology on how to design and install 

forested buffers to protect water quality.

The USDA Forest Service has conducted 

extensive research on reforestation restoration 

techniques, their costs, and expected benefits 

(Gardiner and Oliver 2005). The majority of 

reforestation projects in the Lower Mississippi 

Alluvial Valley (LMAV) use low intensity (less 

expensive, but less assured in obtaining desired 

benefits) methods that were established through 

the CRP and the Wetland Reserve Program 

(Gardiner and Oliver 2005). These programs 

provide subsidies for landowners willing to 

convert agricultural land to forest, range from 

ten year agreements to perpetual easements, and 

reimburse landowners for 75% to 100% of the 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 45

Federal Hypoxia and Watershed Science Research

costs of approved practices. By 2007, reforestation 

reclaimed an estimated 200,000 ha in the LMAV 

(Gardiner and Lockhart 2007) and 75% of this land 

is privately owned (Gardiner and Oliver 2005).

A tool that will help achieve that goal is a 

decision support system that can identify the 

geographic areas with the greatest potential for 

restoration and provision of related ecosystem 

services. The Eco-Assessor, a decision support 

system developed by the USGS and EPA (Davis 

et al. 2002), can help planners and managers 

target areas with the greatest potential for nutrient 

removal from river water by increasing the weight 

of the most important functions in the model 

(water quality) and reducing the weight of less 

important functions (habitat, hydrology, and 

restorability). This can allow managers to target 

areas where the probability of restoration success 

is highest, and eliminate from consideration areas 

with less potential. This can sustain public support 

for wetland restoration by having the most accurate 

information available to the public. 

3.5. Economic Assessments

Determining the economic impacts of coastal 

hypoxia and the costs and benefits of nutrient 

reduction within watersheds has proven difficult 

and complex. However, some progress has 

been made and efforts are ongoing. Within the 

watershed, the USDA Economic Research Service 

(ERS) evaluated the economic costs of reducing 

nutrient loads to the Gulf of Mexico for the original 

Committee on Environment and Natural Resources 

(CENR) study (Doering et al. 1999). Since then, 

ERS has provided some additional insights on 

policy options for reducing nutrient loads to the 

Gulf. In 2001, ERS compared source reduction 

(fertilizer management) and interception strategies 

(wetland restoration) for controlling nitrogen 

loss in the Mississippi River basin (Ribaudo et 

al. 2001). ERS found that a standard on fertilizer 

applications was more cost-effective than restoring 

wetlands up to a particular level of total nitrogen 

loss reduction (about 26% reduction). Beyond this 

point, wetland restorations are more cost-effective. 

In 2005 ERS assessed the economic benefits of 

a water quality trading program between point and 

agricultural sources in the Mississippi River basin 

(Ribaudo et al. 2005). Allowing trades between 

point and agricultural sources was found to reduce 

overall nitrogen abatement costs. A geographically 

extensive trading program was also found to raise 

crop prices, increase production, erosion, and 

nutrient loss outside of the basin.

Additionally, there are ongoing efforts to link the 

watershed models with the USDA REAP (Regional 

Environment and Agricultural Programming) 

economic model developed by USDA (NOAA). 

This linkage will allow for analyses of the 

economic costs of varying management scenarios 

and the corresponding benefits in reducing nutrient 

inputs

As indicated in Section 3.3.2, limited knowledge 

of the ecological impacts of hypoxia on living 

resources has restricted analyses of the economic 

impacts of hypoxia to coastal communities. 

However, a recent bioeconomic model developed 

to examine hypoxia in the Neuse River estuary in 

North Carolina indicates the economic impacts 

of hypoxia may be high (NOAA). The model 

indicates that reductions in the spatial and 

temporal extent of hypoxia could increase profits 

to shrimpers, assuming no additional entry into the 

fishery was permitted. Preliminary estimates from 

this model have suggested that a 30% reduction 

in the number of hypoxic days in the Neuse 

River estuary could potentially increase shrimper 

profits by $2.5 million annually. As knowledge 

of the population and physiological impacts of 

hypoxia grows, it is anticipated that the economic 

consequences will become clearer. 

Scientific Assessment of Hypoxia in U.S. Coastal Waters 47

Future Research Directions 

and Interagency Coordination

Chapter 4

4.1. Introduction

Federal research programs are addressing many aspects of eutrophication, nutrient 

enrichment and hypoxia. Despite decades 

of research, however, management efforts to 

reduce nutrients—particularly from nonpoint 

sources—and their adverse impacts on coastal 

ecosystems have not made significant headway, in 

part due to increased development and population 

in coastal watersheds. The task of managing 

nutrients and associated hypoxia within and across 

diverse landscapes and political jurisdictions is 

complicated by a growing, but still incomplete, 

understanding of the status of eutrophication of 

coastal ecosystems and the processes that control 

water quality responses to excess nutrients. But 

there are significant opportunities for advancement. 

Scientific data and tools are, as of yet, 

inadequate to fully inform management 

actions directed at hypoxia in all of the coastal 

environments impacted by hypoxia. Ideally, such 

tools would allow managers to readily establish 

reasonable science-based goals by quantitatively 

linking management actions to nutrient loads, 

nutrient loads to coastal water quality, and coastal 

water quality to ecological outcomes of concern.

This chapter brings together conclusions of 

a number of reports that independently address 

research endeavors that could best improve 

management of hypoxia in U.S. coastal waters. 

These reports resulted from deliberative, inclusive, 

and cooperative efforts or workshops focused 

on determining research priorities. Research 

priorities related to hypoxia in the northern Gulf 

of Mexico have received more concerted Federal 

deliberation recently than priorities for other 

systems and have been addressed in at least five 

major reports. These include 1) the 2008 Gulf 

Hypoxia Action Plan (Mississippi River/Gulf of 

Mexico Watershed Nutrient Task Force 2008), 

2) the Hypoxia in the Northern Gulf of Mexico, 

An Update by the EPA Science Advisory Board 

(U.S. EPA 2007), 3) the Gulf of Mexico Hypoxia 

Monitoring Implementation Plan (Gulf of Mexico 

Hypoxia Monitoring Implementation Plan 

Steering Committee 2009), 4) the Science Strategy 

to Support Management Decisions Related to 

Hypoxia in the Northern Gulf of Mexico and 

Excess Nutrients in the Mississippi River Basin

(Mississippi River/Gulf of Mexico Watershed 

Nutrient Task Force 2004), and 5) Nutrient 

Control Actions for Improving Water Quality in 

the Mississippi River Basin and Northern Gulf 

of Mexico (NRC 2008). The Lake Erie Research 

Planning Workshop Report (NOAA 2004) 

addressed research needs for Lake Erie, including 

priorities for addressing hypoxia. The introduction 

to the special issue of the Journal of Experimental 

Marine Biology and Ecology on the Ecological 

Impacts of Hypoxia on Living Resources (Kidwell 

et al. 2009) provides a framework for guiding 

research aimed at assessing the effects of hypoxia 

on living resources. Broad guidance regarding 

research priorities has been suggested by national 

assessments such as the National Estuarine 

Eutrophication Assessment (Bricker et al. 2007). 

Although research is clearly being done to support 

management of eutrophication and hypoxia in 

systems, such as Chesapeake Bay, Long Island 

Sound, Narragansett Bay, and Hood Canal, recent 

documentation of an overall research strategy for 

these coastal ecosystems does not exist.

Some of the identified research needs are 

common across coastal systems or regions of the 

country, but there are also differences. These 

differences result from variability in physical and 

ecological properties and in the research carried 
48 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 4

out to date. Four main categories of research needs 

are identified in this report and discussed below. 

Within each category, system-specific or regional 

differences in research needs are examined.

4.2. Improved 

Characterization and 

Quantification of Hypoxia

Effective management of hypoxia requires 

that the causes, extent, and severity of hypoxia 

be adequately understood and quantified. If the 

causes are not thoroughly understood, effective 

management actions cannot be formulated. 

Adequate monitoring information is required 

to know the scope of the hypoxia problem and 

to understand if hypoxia is expanding or being 

reduced as a result of management actions. 

Adequate quantification of hypoxia is needed for 

individual coastal ecosystems that experience 

recurrent and severe hypoxia (e.g., the northern 

Gulf of Mexico) and for the Nation’s coastal waters 

as a whole.

Causes of hypoxia are relatively well understood 

in some systems (e.g., Chesapeake Bay, Gulf of 

Mexico, Long Island Sound), but there are many 

other U.S. systems that have only relatively 

recently been identified as experiencing hypoxia. 

The general phenomena of transient hypoxia due 

to diel-cycling of dissolved oxygen levels can have 

dramatic consequences, such as fish kills, because 

of its frequency and location of occurrence. This 

phenomenon is probably more widespread and 

problematic than currently documented. Process 

studies are needed to elucidate system dynamics 

and clarify causes. For example, improved 

understanding of how nutrient and sediment 

dynamics contribute to hypoxia will lead to 

better predictive models. Further, it is currently 

hypothesized that some systems have experienced 

regime shifts (e.g., Gulf of Mexico, Chesapeake 

Bay) due to nutrient overloading which has the 

effect of increasing the amount of hypoxia for 

a given load of nutrients. Determining factors 

underlying such changes is important for refining 

models and management actions. Hypoxia models 

provide the ability to test hypotheses about the 

causes (i.e., nutrient levels, freshwater flow, 

stratification, sediment dynamics, etc.). Further 

model development and transfer to operational use 

by coastal managers should be pursued. 

Monitoring of hypoxia in U.S. coastal waters 

is currently imbalanced, with some systems 

monitored very well (e.g., Chesapeake Bay) and 

others monitored much less frequently. In some 

cases, a significant effort has been expended, but 

substantial gaps in knowledge remain because the 

affected area is very large and costly to sample 

adequately (e.g., Gulf of Mexico hypoxic zone). 

Monitoring strategies have often been inadequate to 

characterize the incidence of hypoxia because time 

or space scales for sampling are too broad. Further, 

in some waters, hypoxia occurs periodically and 

primarily (or exclusively) at night and cannot be 

captured with regular boat surveys during the day. 

4.2.1. Hypoxia Surveys

Hypoxia is often difficult to quantify since 

there is usually considerable temporal and spatial 

variability. Multiple surveys within a season are 

usually required to assess goals or standard in 

a scientifically valid manner and are critical for 

measuring progress and supporting long-term 

adaptive management strategies. For example, 

the extent of hypoxia in the Chesapeake Bay 

mainstem is monitored by Maryland, Virginia, and 

EPA at least monthly throughout the summer. This 

sampling design allows for an accurate assessment 

of the extent of the problem and has helped 

managers set dissolved oxygen criteria for the Bay 

and track progress toward meeting those criteria. 

In the northern Gulf of Mexico, however, one midsummer shelf-wide survey is conducted by the 

Louisiana Universities Marine Consortium as part 

of NOAA’s NGOMEX research program. Given 

the considerable variability of hypoxia during 

the summer in this region, one cruise does not 

provide the coverage needed to monitor progress 

toward the hypoxia reduction goal. Regularly 

scheduled shelf-wide monitoring of the northern 

Gulf of Mexico during the warmer months of April 

through September would provide the rigorous 

quantification of hypoxia that is required to assess 

the goal on an annual basis. This need has been 

documented in response to a summit that was held 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 49

Future Research and Coordination

to address the current deficiencies in monitoring the 

hypoxic zone in the northern Gulf of Mexico (Gulf 

of Mexico Hypoxia Monitoring Implementation 

Plan Steering Committee 2009).

Although the Chesapeake Bay and some other 

systems (e.g., Long Island Sound) have been 

relatively well-sampled, there is no national 

program or strategy to systematically assess the 

extent, duration, frequency, or intensity of hypoxia 

in U.S. coastal waters. A survey program or 

coordinated monitoring network designed with an 

appreciation of the temporal dynamics and likely 

spatial distribution of hypoxia would provide a 

more complete representation of the extent of 

hypoxia nationwide. 

4.2.2. Instrumented Observing Systems

Ship-based surveys cannot reasonably address 

the extent of hypoxia in all U.S. coastal waters due 

to cost and, particularly, because of the temporal 

dynamics of hypoxia in some coastal systems. This 

challenge can likely be met by new technologies 

for measuring dissolved oxygen, particularly 

optical sensors, that can be deployed in the field 

to provide continuous measurements. Sensors 

are increasingly stable in their calibrations and 

resistance to biofouling. Their data can be relayed 

to investigators in near real-time via wireless 

data networks and other telemetry technologies. 

Instrumented observing systems require an initial 

infrastructure investment, but then may offer costsavings relative to traditional surveys. Moreover, 

only continuously deployed instruments offer 

a practical means of characterizing temporal 

dynamics of hypoxia over a range of time scales, 

including diel-cycling hypoxia. Finally, in situ

observing in the Gulf of Mexico presents special 

consideration. The frequency of hurricanes makes 

maintaining instrumented observing systems 

expensive due to the high cost of insurance and 

replacement costs when devices are lost in major 

storms; such expense is not feasible for most 

academic researchers. Only a Federal partnership 

with state and regional entities is likely to succeed 

in establishing and maintaining a comprehensive 

national monitoring capability for hypoxia. 

4.2.3. Other Advanced Technologies

Autonomous underwater vehicles, such as 

gliders and powered underwater vehicles, can carry 

sensor payloads and provide valuable information 

on the spatial distribution of hypoxia and related 

water quality variables. Like moored instrumented 

observing systems, they may generate cost savings 

by automating sampling and reducing the need for 

costly ship and boat operations. Hypoxia cannot 

be monitored directly via satellite remote sensing, 

but greater use of remote sensing could provide 

important data on factors that cause or control 

hypoxia, including chlorophyll-a, water clarity, 

suspended solids, and potentially other variables. 

Integration of adequate real-time data streams into 

operational nowcast-forecast simulation modeling 

systems (e.g., NOAA PORTS models in Mobile 

Bay, Narragansett Bay, and elsewhere) has the 

potential to provide both spatially and temporally 

An important tool for oceanographic research and water quality 

sampling - the CTD rosette.

Photo: EPA Gulf Ecology Division
50 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 4

resolved characterizations of hypoxia in coastal 

waters with reasonable and quantifiable accuracy.

4.2.4. Improved Modeling of Hypoxia

Because hypoxia results from interactions 

between physical and biological processes in time 

and space, simulation models—especially coupled 

physical-biological water quality models—are 

especially useful. Scientists increasingly rely on 

models to test assumptions about the causes of 

hypoxia. In the past several decades, the technical 

difficulty, cost to implement, and computational 

requirements for running these models and 

evaluating their output have limited their use to 

a few relatively well-funded modeling programs, 

usually working in the highest profile areas (e.g., 

Chesapeake Bay). Recently, this situation has 

begun to change dramatically. Desktop computers 

today are vastly more powerful than they were 

a few years ago. Powerful parallel computing 

clusters can also be assembled at reasonable 

cost. Although the models remain complex, it is 

now possible for more investigators to consider 

implementing and using them. New and efficient 

open-source modeling codes such as ROMS 

(Shchepetkin and McWilliams 2005) and the Finite 

Volume Community Ocean Model (FVCOM) 

(Chen et al. 2006) offer powerful and advanced 

capabilities such as data assimilation, while also 

enabling relatively simple tests of concepts (e.g., 

Hetland and DiMarco 2008). The data needed to 

support the models can increasingly be obtained, 

sometimes in real-time or near real-time via 

internet data portals. It now seems possible 

that even reasonably complex models could be 

developed and used to support water quality 

management and other public needs in many 

coastal systems, or potentially the entire U.S. coast.

Another consequence of the lower cost of 

implementing simulations models is that it is now 

possible and even desirable for several independent 

or “competing” modeling efforts to address similar 

issues for the same geographic location. This 

development is a positive one because scientific 

debate and consensus-building—which promote 

scientific advancement—cannot occur effectively 

if there is only a single modeling program. As an 

example, scientists working to address hypoxia 

in the northern Gulf of Mexico clearly indicated 

their preference for using a variety of different 

models relying on different approaches and 

assumptions (Mississippi River/Gulf of Mexico 

Watershed Nutrient Task Force 2004). The Federal 

government should continue to support modeling 

efforts by supporting open-source model code 

development, programs that maintain large-scale 

modeling efforts, and programs that provide data 

products that facilitate development of local-scale 

water quality models.

4.3. Improved 

Characterization of Impacts 

of Hypoxia

Concern with hypoxia stems from the associated 

loss of human and aquatic life uses in affected 

coastal systems. To set reasonable objectives 

for management of hypoxia, and to justify and 

sustain efforts to achieve those objectives, it is 

important to quantify the impacts, both in terms of 

aquatic life use and ecosystem services provided to 

humans. Further, it is important to quantify losses 

that have or are presently occurring, those that 

will result from a further increase in hypoxia, and 

those ecosystem services that could be restored by 

reducing hypoxia. 

A known continuum of hypoxia effects has 

been empirically related to dissolved oxygen 

concentrations (e.g., Diaz and Rosenberg 1995; 

Kidwell et al. 2009), providing guidance on likely 

effects of hypoxia, even in the absence of direct 

studies of effects in a particular coastal system. 

However, direct and systematic assessments of 

ecological effects of hypoxia in coastal ecosystems, 

which are important for accurately evaluating 

impacts, are relatively rare. Dramatic and visible 

fish kills associated with hypoxia can garner 

significant public attention, but more serious effects 

are often much less obvious, such as reduced 

production. In systems subject to increases in 

hypoxia over time, the public and even scientists 

can fail to recognize both what has been lost and 

what could be regained by restoring water quality.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 51

Future Research and Coordination

4.3.1. Impacts Surveys

Priority research needs related to impacts 

of hypoxia in coastal waters focus on: 

1) characterizing current and past biological 

condition in ecosystems affected by hypoxia 

2) characterizing chronic, sub-lethal effects on 

individuals, 3) quantifying effects at the population 

and community level, and 4) characterizing 

interactions between hypoxia and other stressors. 

Characterizing biological condition of coastal 

ecosystems, such as via faunal assessments, is 

one of the most direct ways to evaluate ecological 

impacts due to hypoxia. Improved faunal 

monitoring presents an opportunity to increase our 

understanding. In the northern Gulf of Mexico, 

NOAA SEAMAP conducts trawl surveys to assess 

fish abundance, but does not examine benthic 

community condition. In some less-studied 

systems where hypoxia has been documented 

(e.g., Pensacola Bay, Florida), very little data are 

available to characterize biological condition, and 

no substantial attempt has been made to relate 

condition to the extent of hypoxia. These data 

limitations contrast with more extensive studies 

in the Chesapeake Bay system, where decades of 

benthic and fish surveys describe the effects of 

hypoxia.

4.3.2. Assessing Biological Responses 

and Modeling

Models are invaluable tools for quantifying 

the effects of hypoxia, sometimes providing 

insights into biotic effects of hypoxia that 

would be impossible to resolve from empirical 

observations alone. Studies that provide a detailed 

understanding of the effects of low oxygen on 

biota present an opportunity to better support 

these models and increase what can be learned 

from them. For example, motile species can 

sometimes avoid exposure to hypoxia by moving 

away. Species may also modify feeding and 

other behaviors, impacting growth, reproduction, 

and often predator avoidance. Further research 

describing these behaviors would support better 

models to predict effects of hypoxia on individuals, 

populations, and communities. Quantification of 

shifts in energy flows within entire food webs as 

a result of eutrophication and hypoxia (e.g., Baird 

et al. 2004) would provide integrated perspectives 

on the effect of hypoxia on marine life in coastal 

systems. Unfortunately, hypoxia is rarely the 

only stressor in coastal systems. Therefore, better 

data and models are needed to examine hypoxia 

interactions with additional stressors such as 

fisheries exploitation, habitat loss, and invasive 

species. Finally, development of bio-economic 

models could help assess effects of hypoxia 

on economically important fisheries and other 

ecosystem services, thereby helping provide an 

improved understanding of the possible economic 

benefits from nutrient management.

4.3.3. Assessing Economic Impacts

For accurate economic analyses, data are 

needed that account for the many sources of 

variability influencing population dynamics and 

landings. In addition, more knowledge on hypoxia 

occurrence and distribution as well as data on 

effects on various ecosystem components are 

needed. Similar limitations are encountered when 

trying to estimate economic losses from HABs 

(Anderson et al. 2000). Long-term monitoring 

programs that measure dissolved oxygen at proper 

spatial and temporal scales coupled with ecosystem 

models described in the previous section are critical 

for resolving the ecological impacts that then 

set the stage for assessing the economic impacts 

attributable to hypoxia. 

4.4. Quantifying Nutrient 

Flux to Coastal Waters

Freshwater inflow and nutrient inputs to coastal 

waters are the primary causes of eutrophication and 

hypoxia in coastal waters. These factors remain 

important areas of uncertainty for coastal science 

and management. Poor quantification of these 

factors makes it much harder to relate hypoxia 

and the associated water quality effects in coastal 

waters to the specific anthropogenic causes in their 

drainage basins. Tracking nutrients delivered to 

coastal waters back to source areas and human 

activities on the landscape is essential for designing 

effective management strategies to reduce nutrient 

losses within the drainage basins and to reduce 

nutrient delivery to coastal systems. Additionally, 
52 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 4

it is important to quantify the environmental 

processes that influence transport and fate of 

nutrients within basins as they affect ultimate 

delivery to coastal ecosystems.

4.4.1. Monitoring Nutrient Sources and 

Fluxes to Coastal Ecosystems 

Monitoring streamflow and nutrient fluxes 

theoretically is straight-forward. Load estimates 

can be made using well-established regressionbased models (Cohn et al. 1992; Runkel et al. 

2004) or related methods (Aulenbach and Hooper 

2006) that rely on streamflow monitoring data and 

regular measures of water chemistry. However, the 

number of gauged rivers is small, and contributing 

drainage basins can extend over broad areas quite 

distant from the coast. As a result, significant 

monitoring is required to provide sufficient data 

to make adequate estimates of the delivery of 

streamflow and nutrients to the coast and the source 

areas and human activities within the basin that 

affect them.

Although simple in theory, there remains 

room to improve the statistical methods of 

load estimation directed largely at reducing the 

frequency and costs associated with water quality 

monitoring. Nutrient load estimates with adequate 

temporal resolution to develop cause-and-effect 

linkages to the onset, extent, and duration of 

hypoxia and to support empirical and simulation 

models of coastal systems currently are not 

available in the United States. This is largely a 

result of insufficient frequency of water quality 

monitoring and inadequate streamflow gauging. 

Acceptably accurate estimates of loads are needed 

at monthly or higher frequencies (e.g., weekly). 

However, increased temporal resolution comes 

at the expense of increased limits of uncertainty 

unless there is a commensurate increase in the 

frequency of sampling. 

Continuous real-time nutrient monitoring 

stations offer a potential solution. These have been 

pioneered in a few locations such as the mouths of 

the Mississippi and Atchafalaya Rivers. However, 

the technology needs further development to be 

more practical and reliable and to provide data on a 

sufficient suite of water quality constituents. 

Monitoring riverine delivery of nutrients 

beyond tidal waters to coastal systems has been 

complicated by difficulties in stream gauging and 

representative sampling in tidal reaches. New 

techniques employing acoustic doppler current 

profilers have made these measurements possible 

and reduced the uncertainty associated with 

nutrient removal or additions in tidal river reaches 

(Box 13). 

Measurements of point source loadings of 

nutrients are also needed. For most coastal 

waters, these are not sufficiently accessible. 

The Chesapeake Bay Program’s Nutrient Point 

Source Database provides a good example of 

what should be implemented much more broadly. 

A consistent, systematic, and comprehensive 

nationwide approach for estimating nutrient 

loads to coastal waters from all upland sources 

(fluvial, diffuse, point source, atmospheric) would 

be a very valuable tool to support science and 

management related to hypoxia in U.S. coastal 

Dr. Peter Eldridge extracts sediment cores to investigate 

sediment biogeochemical processes in the Gulf of Mexico 

hypoxic zone.

Photo: EPA Gulf Ecology Division
Scientific Assessment of Hypoxia in U.S. Coastal Waters 53

Future Research and Coordination

waters. Estimates for atmospheric deposition, both 

dry and wet, to coastal systems is a source of great 

uncertainty in the understanding of nitrogen and 

carbon cycling in watersheds.

4.4.2. Modeling Source Areas, Source 

Mechanisms, and Trends in Nutrient 

Loads 

Modeling is a valuable tool for interpreting 

data across a broad range of scales and employing 

a range of approaches from purely deterministic 

simulation modeling to statistically based empirical 

approaches. 

The interpretation of trends in streamflow 

and nutrient loads provides important feedback 

to adaptive management. Separation of natural 

variations from those induced by human activities, 

such as changes in land use practices and 

management actions to reduce nutrient loses, can 

be extremely challenging. New statistical models 

are needed to implement such time series analyses. 

There are insufficient resources to monitor 

streamflow and nutrient loads at all inland 

watersheds. As a result, monitoring is done in 

watersheds representative of others with similar 

climate, land use, other measures of nutrient inputs, 

wetlands, and management actions. In turn, the 

models help identify the representative watersheds. 

The models then extend the monitoring data across 

the entire basin to show the different contributions 

geographically and to identify the relative 

contributions from different anthropogenic sources. 

Such spatial information should be considered 

when management actions are implemented so 

that resources are invested where they will have 

the greatest benefit. Although the SPARROW 

model has been applied at a national scale (Smith 

et al. 1997), as well as regional (e.g., Preston and 

Brakebill 1999, Moore et al. 2004) and smaller 

scales, one limitation of SPARROW is that it has 

been applied to estimate average annual loading. 

Other approaches are needed where seasonal or 

interannual differences must be resolved. Isolated 

implementation of models, such as Hydrological 

Simulation Program-Fortran, can meet this need, 

but it has not been developed for most of the 

Nation’s estuaries. 

Ancillary data on human activities across 

the landscape that affect nutrient inputs are 

critical to the development of models that 

extend monitoring data across large contributing 

drainage basins. These ancillary data include 

information on chemical use, land use, and 

information on the types and distribution of 

management actions intended to mitigate nutrient 

losses to streams. The data include type of crop 

or animal agriculture; the extent, pattern, and 

intensity of agricultural drainage; the extent of 

riverine ecosystems that affect instream nutrient 

concentrations; and improved estimates of direct 

nutrient inputs (atmospheric deposition and point 

source discharges). Furthermore, to make accurate 

projections of future trends, research is needed 

to improve understanding of the consequences of 

long-term drivers, such as climate change, changes 

in cropping systems, extent of tile drainage, and 

biofuels production.

Groundwater also can provide a significant 

contribution of water and nutrients to coastal 

waterbodies. It is difficult to quantify these 

flows and loads. Although ground-water flow 

system models can improve estimates of these 

contributions, they are difficult and expensive 

to develop. Cost-effective models are needed to 

assess the relative role of ground water in coastal 

ecosystems and to quantify its contribution where 

significant.

4.4.3. Nutrient Processes in Watersheds 

Quantification of the biogeochemical processes 

that affect nutrient transport on the landscape and 

within streams will also support development 

of sound land and water quality management 

practices. These processes affect how nutrients 

are transported from lands with various land use 

practices (crop agriculture, animal agriculture, 

urban, suburban) to streams and include 

various components of the hydrologic cycle 

(runoff, groundwater seepage, tile drainage, and 

atmospheric transport). Biogeochemical processes 

determine nutrient transport and persistence 

downstream to receiving waters, including nutrient 

transformation and removal. Ecosystem types that 

are most effective at reducing instream nutrient 
54 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 4

loads and the characteristics that make them most 

efficient must be identified. These include riverine, 

estuarine, coastal, wetland, and delta ecosystems. 

Research is needed on small watersheds to 

integrate understanding of the source of nutrients; 

the role of groundwater, surface waters, riparian 

zones and wetlands in the transport of nutrients 

to the stream; and the downstream persistence 

of nutrients. A better understanding is needed of 

the temporal and seasonal variation in nutrient 

fluxes and the time lags associated with changes in 

drivers (increased inputs or mitigation measures) 

and resulting changes in nutrient loads. The role 

of various environmental media (sediment and 

organic matter) in defining nutrient budgets is 

poorly understood. Improved approaches are 

needed to characterize water and nutrient balances 

for land areas to which mitigation measures may 

be applied to ensure that resources are invested 

in the highest priority areas and to areas where 

management actions will have the greatest effect on 

nutrient loads to receiving coastal waters. 

Most research on nutrient cycling in watersheds 

is driven largely by concerns for science-based 

management actions that improve local water 

quality conditions. Typically, this research is not 

driven by concerns for water quality effects on 

coastal ecosystems, which can be quite distant—

both geographically and culturally. An important 

goal of research on nutrient processes that is 

pertinent to hypoxia should be to consider aspects 

that are important to downstream receiving waters. 

4.5. Approaches for 

Reducing Nutrient Inputs to 

Coastal Waters

This research is directed at developing improved 

management tools for mitigating excessive nutrient 

fluxes to coastal ecosystems. It has two major 

components: 1) reducing nutrient inputs – research 

to identify BMPs for reducing nutrient inputs to 

streams, including losses from agricultural lands, 

point source inputs, urban/suburban runoff, and 

atmospheric deposition; and 2) enhancing nutrient 

removal – research to identify the instream nutrient 

reductions taking place in wetland areas, including 

reconstructed wetlands, river reaches amenable to 

nutrient removal processes, constructed riverine 

wetlands, and coastal diversions. Process research 

on nutrient cycling and transport is fundamental to 

both of these components. Understanding where 

nutrients are entering the watershed and how much 

each region is contributing will lead to more costeffective targeting of nutrient reduction strategies. 

4.5.1. Evaluation of Nutrient Reduction 

Strategies

Evaluations of nutrient reduction strategies 

should continue in a deliberate and measurable 

way to promote the most efficient and costeffective management alternatives. CEAP (see 

Section 3.4.1.2) is already proving to be a good 

tool for this purpose and may warrant expansion 

to more regions of the United States. CEAP and 

other scientific assessments should be continued 

to evaluate the effectiveness of current nutrient 

reduction management techniques, while 

developing ways to maximize their effectiveness 

Box 13. USGS Deployment of New 

Instruments to Measure Water Flow 

and Sediment Flux

USGS is now deploying acoustic doppler current 

profilers on a variety of platforms to monitor a range of 

hydrologic measurements and applications, including 

computing continuous records of streamflow for tidally 

or backwater affected streams, measuring velocity fields 

with high spatial and temporal resolution, and estimating 

suspended-sediment concentrations.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 55

Future Research and Coordination

and improve implementation and maintenance, 

including market-based environmental stewardship 

programs. Other assessments which should 

improve nutrient reduction management include: 

1) socioeconomic and bioeconomic assessments of 

alternative nutrient management scenarios through 

the development of integrated economic and 

watershed models; 2) more thorough evaluation 

of the efficacy of dual nutrient (nitrogen and 

phosphorous) control practices; and 3) evaluation 

of the most effective ways to market nutrient 

reduction strategies to farmers. Further, the 

importance of seasonality and nutrient form should 

be considered in nutrient reduction strategies. 

Finally, as the understanding of climate change 

impacts becomes more refined, this new knowledge 

needs to be applied to current nutrient reduction 

strategies.

4.5.2. Biofuels Research

Research on biofuel life cycles is needed to 

assess the environmental effects, economics, 

and resource availability of biofuel feedstocks. 

Research has already shown fewer environmental 

impacts if cellulosic feedstocks are used instead of 

corn. Region-specific biofuel production systems 

should be encouraged to maximize production 

while minimizing environmental impacts. “Regionspecific” implies a more localized approach to 

the type of feedstock used for biofuel distillation 

(e.g., considering what grows best where), thereby 

reducing distance between farms and biofuel plants 

and closing the loop on byproducts reuse (e.g., 

feeding corn mash to live stock).

4.5.3. Local Water Quality Concerns

In inland states, there are inherent difficulties in 

developing an appreciation for the implications that 

nutrient inputs to rivers ultimately have on coastal 

ecosystems. Therefore, it is important to consider 

both local and regional water quality concerns 

in nutrient studies and management strategies. 

Studies should consider the implications of excess 

nutrients in local streams and estimate the costs in 

terms of both lost ecosystem services and the local 

and regional benefits associated with improving 

local water quality conditions. Excess nutrients in 

streams, rivers, and lakes can result in a plethora 

of problems, including unsightly algal blooms, fish 

kills, nitrate or ammonia toxicity, and contaminated 

drinking water. The safety standard (maximum 

contaminant level) for nitrate in drinking water 

established by the EPA is 10 mg/L (Ward et al. 

2005). Nitrate levels at or above this level have 

been known to cause a potentially fatal blood 

disorder in infants under six months of age called 

methemoglobinemia or “blue-baby” syndrome. 

Therefore, when selecting nutrient management 

strategies, it is imperative to look for ‘win-win’ 

situations that improve both local and coastal water 

and habitat quality. 

4.5.4. Nutrient Management Technology 

Development

Given the development of new technologies, 

such as the use of remote sensing for new 

applications (which include assessment of crop 

nutrient needs), it is important to continue to 

develop nutrient management technologies (e.g., 

cover cropping, siting of BMPs, stormwater 

controls) to reduce nitrogen and phosphorus 

inputs to the coasts arising from both agriculture 

and urban/suburban sources. Achieving higher 

sequestration of applied nutrients by crops and 

reducing losses from soils without compromising 

agricultural yield should be one of the central 

goals of this research. In general, the science 

and management practices related to control of 

nonpoint nutrient sources is far behind that for 

point sources, such as wastewater treatment plants. 

4.5.5. Improve Natural Nutrient Removal 

Processes

Evaluation and exploration of methods to 

enhance natural processes that remove nutrients 

from streams and rivers should be a high priority. 

Naturally vegetated watersheds, and particularly 

those that contain wetlands, are highly effective 

at nutrient retention and are important in both 

improving and sustaining water quality. Research 

is needed on how to identify the most promising 

land areas and methods to restore the ecosystem 

services provided by vegetated watersheds and 

wetlands. Also, adaptation research is needed to 

increase the resiliency of forests, rangelands, and 

aquatic areas in an effort to mitigate the adverse 
56 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Chapter 4

impacts of climate change. As the understanding of 

ecosystem processes improves, methods to evaluate 

ecosystem services and to develop incentives for 

the public will be needed. 

4.6. Existing and Future 

Coordination 

In the immediate future, there is a strong 

need for improved data access across agencies. 

Access to data is critical for model development. 

Coordinated, consolidated, and improved access 

to data, relevant to particular watersheds and 

to hypoxia in the coastal zone and for use by 

watershed and coastal zone managers, should 

be available across agencies and to the public. 

NOAA provides data access through the National 

Oceanographic Data Center (http://www.nodc.

noaa.gov/) which requires all NOAA-funded 

researchers to deposit data within two years 

of project completion. EPA’s STOrage and 

RETrieval (STORET) data system provides the 

same function for EPA-funded research (http://

www.epa.gov/storet/about.html). USGS data are 

stored in the USGS National Water Information 

System, which has a website for public access 

to the data (http://waterdata.usgs.gov/nwis). 

EPA and USGS have made significant progress 

toward providing scientists and policy makers 

an easier way to integrate access to their large 

water quality databases. A common suite of 

web services allow for the automated sharing of 

water monitoring data via a common format and 

terms (http://qwwebservices.usgs.gov/). USDA’s 

ARS has recently developed STEWARDS 

(http://arsagsoftware.ars.usda.gov/stewards/) as 

a repository for data collected as part of ARS’ 

watershed research network activities towards the 

CEAP croplands initiative. All of the agencies 

need to improve access and usability and provide 

an interface among their various databases.

Growing cooperation among Federal agencies 

and among Federal, state, local, and tribal agencies 

has enhanced hypoxia monitoring and research 

capabilities. Most coastal regions with hypoxia 

problems in the United States now have well 

coordinated, multi-agency, multi-state management 

plans with informed, active science and technology 

advisory committees, many of which evolved 

from the National Estuary Program initiative. 

Some of these regional partnerships have existed 

for decades while others are just forming. For 

instance, the Chesapeake Bay Program (http://

www.chesapeakebay.net/), which was founded in 

1983, engages a range of stakeholders and has been 

responsible for organizing real, tangible actions 

to improve water quality in the Bay. On the other 

hand, the Puget Sound Partnership, which was 

just formed in 2007, is a relatively new effort to 

address the worsening water quality resulting from 

development of the Puget Sound watershed. 

A recently released report (December 2008) 

from the National Research Council of the 

National Academies recommends the creation 

of a Mississippi River Basin Nutrient Control 

Implementation Initiative (NCII) to be established 

jointly within the USDA and EPA (http://www.

nap.edu/catalog.php?record_id=12544). The 

NCII would focus on many of the research 

recommendations outlined in Section 4.6 (e.g., 

pilot studies on nutrient reduction, analysis of costeffective nutrient reduction strategies, etc.), but 

more importantly it would solidify coordination 

between the two Federal agencies primarily 

responsible for improving water quality in 

freshwater U.S. systems.

Ultimately, though, there is no national policy to 

confront the issues of eutrophication and hypoxia, 

and no single Federal agency is in charge of 

coordinating a Federal response. As evidenced 

in this report, coordinated efforts are required 

across at least four major agencies (EPA, NOAA, 

USGS, USDA, as well as others) in order to 

address both the impacts of hypoxia and its root 

causes. Currently, the IWG-4H provides some 

measure of communication and coordination about 

hypoxia across agencies. In addition, interagency 

communication happens through deliberations in 

other IWGs which address related issues, such as 

the sustainable development of biofuels. 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 57

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68 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Appendices
Scientific Assessment of Hypoxia in U.S. Coastal Waters 69

Executive Summary Appendices

Appendix I: Federal Agency Hypoxia or 

Hypoxia-related Research

I.A. Department of Agriculture 

I.A.1. Agricultural Research Service

The Agricultural Research Service (ARS) is an in-house scientific research agency of the U.S. 

Department of Agriculture. ARS conducts research to develop and transfer solutions to agricultural 

problems of high national priority and disseminates information to: 1) ensure high-quality, safe food, 

and other agricultural products; 2) assess the nutritional needs of Americans; 3) sustain a competitive 

agricultural economy; 4) enhance the natural resource base and the environment; and 5) provide economic 

opportunities for rural citizens, communities, and society as a whole.

The Water Availability and Watershed Management National Program is part of Natural Resources 

and Sustainable Agricultural Systems, one of four broad areas for ARS research. The national program 

structure allows ARS to link USDA scientists in laboratories around the country to address research 

problems of local, regional, national, and international interest, such as hypoxia. http://www.ars.usda.gov/

research/programs/programs.htm?NP_CODE=211

The Conservation Effects Assessment Project (CEAP) provides the farming community, the 

conservation community, the general public, the Office of Management and Budget, legislators, and 

others involved with environmental policy issues, with an account of the environmental effects or 

benefits obtained from USDA conservation program expenditures. CEAP is jointly managed by ARS; the 

Cooperative State Research, Education, and Extension Service (CSREES); Farm Service Agency (FSA); 

and Natural Resources Conservation Service (NRCS). http://www.nrcs.usda.gov/TECHNICAL/NRI/ceap/

STEWARDS (Sustaining the Earths Watersheds Agricultural Research Data System) was created 

to house data collected as part of CEAP assessment for croplands. This data system organizes and 

documents soil, water, climate, land-management, and socioeconomic data from multiple agricultural 

watersheds across the United States, allowing users to search, download, visualize, and explore data for 

research and conservation management purposes. The National Agricultural Library, Beltsville, MD, has 

developed a series of six CEAP-related bibliographic databases that are available to the public through 

their website: http://www.nal.usda.gov/wqic/. This dynamic relational database offers more than 5,200 

citations of current research findings from around the globe to help scientists and the public understand 

the environmental effects and benefits of conservation practices implemented through various USDA 

conservation programs. http://arsagsoftware.ars.usda.gov/stewards/. 

I.A.2. Cooperative State Research, Education, and Extension 

Service

CSREES provides Federal assistance in the form of grants for research, education, and extension 

activities related to agriculture. The CSREES Water Program focuses on creating and disseminating 

knowledge that ensures a safe and reliable source of water to meet the needs for food, fiber, and energy 

production; human use and economic growth; and maintenance and protection of natural environmental 

systems and ecosystem services. CSREES’ unique niche is conducting research, education, and extension 

programs to protect and improve water resources in agricultural, rural, and urbanizing watersheds 

(including forest lands, rangelands, and croplands).
70 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

CSREES has been a partner with ARS, NRCS, and FSA in the CEAP. Thirteen watershed projects 

were jointly funded by CSREES and NRCS to evaluate the effectiveness of conservation practices on 

water quality at the watershed scale. These 13 watershed projects serve as examples of collaborative 

work between land grant universities and NRCS. The projects are unique in that they combine evaluation 

of the biophysical effects of conservation practices and the socioeconomic context of the watershed 

location. The watershed projects also combine research and extension/outreach activities – involving 

agricultural producers in project outcomes. Through CEAP, the land grant university system has 

developed substantial capacity to increase the understanding of effects of conservation practices and the 

effectiveness of conservation programs. 

CSREES and NRCS collaborated to fund two projects to synthesize results from the 13 watershedscale projects. These two projects will build a knowledge base to evaluate impacts of conservation 

practices over broad regions, improve management of agricultural landscapes, and inform policy 

decisions at the local, state, and national scale. The two projects differ in their approach – the first uses 

a synoptic overview of the 13 watershed studies and the second uses a modeling framework to spatially 

distribute results from the 13 watershed to broader geographic regions.

CSREES also provides funding for a national network of regional projects that focus on performancebased programs to address water resource issues. The ten regional projects are geographically aligned 

with U.S. EPA regions (see www.usawaterquality.org). These regional projects are directly involved with 

addressing hypoxia through research, education, and extension programs on animal manure management, 

nutrient management, and social and economic policy sciences. They make research, education, and 

extension resources of the university system more accessible to Federal, State, and local water resources 

improvement efforts. Through these projects, new or expanded opportunities develop for agricultural 

producers and agriculturally impacted communities to adopt voluntary approaches for the improvement 

of water resources. They promote delivery of multi-state programming to address regional and/or 

multiregional water quality concerns.

I.A.3. Farm Service Agency

The primary FSA activity related to hypoxia is the Conservation Reserve Program (CRP). CRP is a 

voluntary program available to agricultural producers to help them safeguard environmentally sensitive 

land. Producers enrolled in CRP plant long-term, resource-conserving covers to improve the quality of 

water, control soil erosion, and enhance wildlife habitat. In return, FSA provides participants with rental 

payments and cost-share assistance. Contract duration is between 10 and 15 years.

CRP protects millions of acres of American topsoil from erosion and is designed to safeguard the 

Nation’s natural resources. By reducing water runoff and sedimentation, CRP protects groundwater and 

helps improve the condition of freshwater and marine resources. Acreage enrolled in the CRP is planted 

with resource-conserving vegetative covers, making the program a major contributor to increased wildlife 

populations in many parts of the country. http://www.fsa.usda.gov/FSA/webapp?area=home&subject=cop

r&topic=crp

I.A.4. U.S. Forest Service

The USDA Forest Service (http://www.fs.fed.us/research/) has a mission to sustain the health, 

diversity, and productivity of the Nation’s forests and grasslands to meet the needs of present and future 

generations. The research and development arm of the Forest Service works at the forefront of science to 

improve the health and use of our Nation’s forests and grasslands. Today, more than 500 Forest Service 

researchers work across the 50 states, U.S. territories, and commonwealths in a range of biological, 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 71

Executive Summary Appendices

physical, and social science fields to promote sustainable management of the Nation’s diverse forests 

and rangelands and the ecosystem services they provide. The work has a steady focus on informing 

policy and land management decisions, including those on degraded river ecosystems. The researchers 

work independently and with a range of partners, including other agencies, academia, nonprofit groups, 

and industry. The information and technology produced through basic and applied science programs is 

available to the public for its benefit and use.

With over two-thirds of the Nation’s freshwater originating on forested lands, the role of the Forest 

Service to manage and restore watersheds is indispensable. The Forest Service works to improve 

management practices and techniques, develop best management practices that are cost-effective, 

and lead efforts in the advancement of markets and payments for ecosystem services. In addition, the 

Forest Service is working to develop methods for assessing changes in watershed condition as a result 

of changing demographics and development pressures. The Forest Service has developed a national 

strategy for consistent characterization of watershed condition. The characterization will be used to 

prioritize, identify and implement integrated watershed-scale improvement projects on National Forests. 

Phase 1 will determine the initial (baseline) watershed condition on National Forest System lands using 

consistent, broadly available data. Phase 2 is a six-step process for classifying watersheds at a finer scale 

and prioritizing them for treatment, identifying integrated projects that would move them into improved 

condition classes. Phase 3 involves validating and monitoring watershed condition. 

I.A.5. Economic Research Service

The Economic Research Service (ERS) is the main source of economic information and research 

from USDA. It brings the perspective of economic analysis to critical issues confronting farmers, 

agribusiness, consumers, and policy makers. In general, ERS’s data program collects information that can 

be used in an assessment of policy options in the Mississippi Basin. In conjunction with USDA National 

Agricultural Statistics Service, ERS collects data through the Agricultural Resource Management Survey 

on production practices, conservation practices and input use for major crops in major crop producing 

states. ERS uses these and other data to routinely report on the status and trends of water resource 

indicators such as tillage practices, conservation practices, chemical input use, and conservation program 

expenditures for water quality and water conservation. http://www.ers.usda.gov/

I.B. Department of Commerce

I.B.1. National Oceanic and Atmospheric Administration

I.B.1.a. National Ocean Service 

National Centers for Coastal Ocean Science, Center for Sponsored Coastal Ocean Research

Gulf of Mexico Ecosystems and Hypoxia Assessment Program (NGOMEX). To address the issue of 

hypoxia in the northern Gulf of Mexico, NOAA’s Center for Sponsored Coastal Ocean Research supports 

multi-year, competitive, interdisciplinary research projects to develop a fundamental understanding of the 

northern Gulf of Mexico ecosystem with a focus on the causes and effects of the hypoxic zone and the 

prediction of its future extent and impacts. The research program, which began in 2003 as a result of the 

HABHRCA 1998 legislation, focuses on developing a predictive capability for the Louisiana continental 

shelf ecosystem within an adaptive management framework by connecting monitoring, data analysis, 

model predictions, and management actions with continuous feedback for improvement. Current studies 
72 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

are documenting the dynamics of the hypoxic zone over the Louisiana continental shelf and helping to 

better define the biological, chemical, and physical processes that influence hypoxic zone development 

and determine its extent, and impacts on fisheries. http://www.cop.noaa.gov/stressors/pollution/current/

gomex-factsheet.html

Coastal Hypoxia Research Program (CHRP). The purpose of the CHRP program, which awarded 

its first research grants in 2005, is to expand NOAA’s research capability to address hypoxia in other 

regions experiencing hypoxia beyond the northern Gulf of Mexico. This program is providing research 

results and modeling tools to help coastal resource managers assess alternative management strategies 

and make informed decisions for preventing or mitigating the impacts of hypoxia on coastal ecosystems. 

Determining the causes of hypoxia, developing the capability to predict its occurrence in response to 

varying levels of anthropogenic stress, and evaluating the subsequent ecological, economic, and social 

impacts are necessary to assess potential management alternatives.

Key areas of CHRP research include: 1) the development of a predictive capability for the spatial and 

temporal extent of hypoxia given current and potential anthropogenic and natural forcing scenarios and 

potential management alternatives, 2) the determination of the current ecological and economic impacts 

of hypoxia in a region, 3) the development of ecological forecasts and economic valuations of the impacts 

of changes in a hypoxic region’s spatial or temporal extent, and 3) the development of models that predict 

the susceptibility of coastal systems to the formation of hypoxic waters, thereby allowing managers to 

better focus monitoring and assessment programs which should result in more efficient and successful 

protection and restoration efforts. http://www.cop.noaa.gov/stressors/pollution/current/gomex-factsheet.

html

National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment 

NOAA’s Center for Coastal Monitoring and Assessment recently completed an ambitious update to 

the National Estuarine Eutrophication Assessment (http://ccma.nos.noaa.gov/publications/eutroupdate), 

which assesses nutrient conditions and direct/indirect impacts in U.S. estuaries. The report thoroughly 

analyzed available data and assigned condition rankings to estuaries. Geographic accounts of hypoxia 

are included in the report. Changes in eutrophication status since the last assessment give a sense of the 

growing incidences of hypoxia in coastal waters.

Office of Ocean and Coastal Resource Management

National Estuarine Research Reserve System (NERRS). The principal mission of the NERRS 

System-Wide Monitoring Program (SWMP) is to develop quantitative measurements of short-term 

variability and long-term changes in the water quality, biotic diversity, and land-use/land -cover 

characteristics of estuaries and estuarine ecosystems for the purposes of contributing to effective coastal 

zone management. Long-term monitoring and iterative habitat assessments conducted within the network 

of 27 NERRS sites are intended to improve the fundamental understanding of the temporal and spatial 

dynamics of estuarine processes, and to provide baseline information to evaluate subsequent changes 

in the ecological status of estuarine ecosystems in response to natural perturbations and anthropogenic 

disturbance. Federal coordination of the NERRS SWMP allows for the recognition of significant 

ecological trends (improvement or degradation) in estuaries at national, regional, and local levels. 

Moreover, continued operation of the long-term monitoring effort within the network of representative 

NERRS sites will provide valuable data to inform assessments and/or models on the cumulative effects 

of environmental stressors in estuarine ecosystems located throughout the U.S. coastal zone. Monitoring 

at each SWMP site includes continuous measurements of dissolved oxygen levels and monthly nutrient 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 73

Executive Summary Appendices

sampling. Between 2005 and 2007, NERRS organized the SWMP data into several regional reports, 

including for the Northeast, Mid-Atlantic and the Pacific coast.

I.B.1.b. Oceanic and Atmospheric Research 

Great Lakes Environmental Research Laboratory 

NOAA’s Great Lakes Environmental Research Laboratory, in collaboration with researchers from the 

United States and Canada, is undertaking one of the largest, most comprehensive Lake Erie research field 

programs ever. The International Field Years on Lake Erie (IFYLE) program, which started in 2005 and 

is projected to continue through 2010, aims to improve understanding of large-scale (time and space) 

driving forces of ecosystem dynamics. The project has a special research focus on hypoxia and harmful 

algal blooms and their impacts in Lake Erie.

National Sea Grant College Program

The National Sea Grant College Program is a competitive awarded research program which leverages 

state participation with Federal funds. It has focused some research funding on hypoxia research, 

specifically in the Southeast coastal states.

I.B.1.c. National Marine Fisheries Service

NOAA National Marine Fisheries Service (NMFS) conducts fish surveys/mapping of the entire Gulf 

coast, with bottom dissolved oxygen as one of the measured parameters, in late June/early July and then 

again in early September as part of its routine Southeast Area Monitoring and Assessment Program’s 

(SEAMAP’s) groundfish surveys. The dissolved oxygen data are provided to the public via the Gulf 

of Mexico Hypoxia Watch website (http://ecowatch.ncddc.noaa.gov/hypoxia), which is managed by 

NOAA’s National Environmental Satellite, Data, and Information Service. NOAA NMFS scientists 

have also studied the impact of hypoxia on Gulf coast fisheries. NMFS has also added dissolved oxygen 

monitoring to its salmonid surveys along the Pacific Northwest to monitor hypoxia on the continental 

shelf.

I.C. Department of Defense

I.C.1. U.S. Army Corps of Engineers

System-Wide Water Resources Program (SWWRP). The U.S. Army Corps of Engineers (USACE) 

is developing watershed, regional, and system-wide assessment tools that are applicable to nutrient and 

sediment assessments and decision support. As part of the SWWRP, one-, two, and three-dimensional 

hydrologic, hydrodynamic, and water quality models have been developed and demonstrated in various 

watershed, riverine, reservoir, and estuarine applications. Example applications include assessment 

of nutrient and sediment loading in the upper Eau Galle, Wisconsin, watershed and hydrodynamic 

assessments in the Upper Auglaize, Ohio, watershed. Basic research in nitrogen dynamics has been 

done in conjunction with pool fluctuations in the Upper Mississippi River. Response in reservoir water 

quality to loadings has been studied in numerous USACE reservoirs. Response to nutrient and sediment 

loads in estuaries has been assessed in the Chesapeake Bay. Data management and visualization tools 

using CorpsGlobe (developed with Google Earth technologies) have been fielded for displaying multidimensional modeling results in a geospatial and temporal context for decision support.
74 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Chesapeake Bay Environmental Model Package (CBEMP). The CBEMP is the product of a twentyyear partnership among the USACE Baltimore District, the USACE Engineer Research and Development 

Center, and the EPA Chesapeake Bay Program. The CBEMP is a coupled system of models aimed and 

managing and reducing eutrophication in the Bay. In particular, the model is aimed at restoring living 

resources, reducing anoxia, and improving water clarity. The present phase of the study continues 

the partnership and is focused on the simulation of suspended solids and living resources interactions.

The current focus is to assess how management of suspended solids in the watershed may improve 

Chesapeake Bay water quality and remove water quality impairments, such as low dissolved oxygen, 

algal blooms, and poor water clarity. USACE has completed an initial calibration with runs of various 

management scenarios and is revising the model based on the results of the initial scenarios.

I.D. U.S. Environmental Protection Agency

I.D.1. Regional Offices

Great Lakes National Program Office

The EPA Great Lakes National Program Office (GLNPO) brings together Federal, state, tribal, local, 

and industry partners in an integrated, ecosystem approach to protect, maintain, and restore the chemical, 

biological, and physical integrity of the Great Lakes. In respect to hypoxia, the program monitors Lake 

ecosystem indicators, such as dissolved oxygen, and manages and provides public access to Great Lakes 

data (http://www.epa.gov/glnpo/monitor.html). Each year, GLNPO uses its funding to assist Great Lakes 

partners in these areas through grants, interagency agreements, and contracts (http://www.epa.gov/glnpo/

fund/glf.html). In 2002, the GLNPO held a funding competition focused specifically on hypoxia in 

western Lake Erie.

Gulf of Mexico Program Office 

The Gulf of Mexico Program was formed in 1988 by the EPA as a nonregulatory, inclusive partnership 

to provide a broad geographic focus on the major environmental issues in the Gulf. The mission of the 

Program is “to facilitate collaborative actions to protect, maintain, and restore the health and productivity 

of the Gulf of Mexico in ways consistent with the economic well-being of the Region.” The partnership 

includes representatives from state and local governments and citizens in each of the five Gulf States; 

the private sector (business and industry); Federal agencies responsible for research, monitoring, 

environmental protection, and natural resource management; and the academic community. This 

partnership has been very effective in providing a mechanism for addressing complex problems that cross 

Federal, state, and international jurisdictional lines; a better coordination among Federal, state, and local 

programs that has increased the effectiveness and efficiency of the long-term commitment to manage and 

protect Gulf resources; a regional perspective to access and provide the information and address research 

needs required for effective management decisions; and a forum for affected groups using the Gulf, public 

and private educational institutions, and the general public to participate in the solution process.

 Through its partnerships, the Program is working with the scientific community; policymakers at 

the Federal, state, and local levels; and the public to help preserve and protect the Gulf. It has made 

significant progress in identifying the environmental issues in the Gulf ecosystem and in organizing a 

program to address those issues. The Program provides a tool to leverage the resources of 18 different 

Federal agencies, a variety of environmentally minded agencies from the states of Alabama, Florida, 

Louisiana, Mississippi, and Texas; and numerous public and private organizations. Spanning the broad 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 75

Executive Summary Appendices

range of environmental concerns from the local to the regional and national presents a significant 

challenge to the agencies and organizations that have partnered under the banner of the Gulf of Mexico 

Program, and the Program has met that challenge.

Chesapeake Bay Program Office

The Chesapeake Bay Program Office represents the Federal government in the implementation of 

strategies to meet the restoration goals of the Chesapeake Bay Program. The Chesapeake Bay Program 

is a unique regional partnership leading and directing restoration of the Chesapeake Bay. Its mission is to 

lead and empower others to protect and restore the Chesapeake Bay ecosystem for future generations.

I.D.2. Office of Water 

Office of Wetlands, Oceans, and Watersheds

The office of Wetlands, Oceans, and Watersheds (OWOW) provides leadership, policy directions, 

and financial support to ten regional offices as well as states, tribes, and territories. OWOW administers 

a number of programs that are directed at reducing nutrient pollution and its resultant impairments in 

watershed and coastal waters. OWOW facilitates states and tribes in the listing of impaired waters, 

which includes those that have been degraded by excess nutrients and are unable to meet the water 

quality standards set by states, territories, or authorized tribes. From this list, OWOW provides assistance 

for the development of total maximum daily loads (TMDLs), each of which is a calculation of the 

maximum amount of pollution that waters can receive and still meet water quality standards. Using 

TMDLs, OWOW is investigating the use of water quality trading programs as a possible way to control 

nutrient pollution. Additional relevant OWOW programs include the nonpoint source program, targeted 

watershed grants, the National Water Quality Inventory, and National Aquatic Resource Surveys. 

OWOW also supports and provides leadership to the Mississippi Watershed/Gulf of Mexico Nutrient Task 

Force Coordinating Committee and participates and provides leadership to the Gulf of Mexico Alliance 

Water Quality and Nutrient Reduction teams. In addition, OWOW manages the Ocean Survey Vessel 

Bold, which supports coastal ocean assessment, monitoring and process-oriented research in U.S. waters, 

including numerous systems impacted by nutrients and hypoxia.

EPA’s National Estuary Program (NEP) was established by Congress in 1987 to improve the quality 

of estuaries of national importance. For information on the NEP, see National and Interagency Efforts, 

Section I.F.3.

Office of Science and Technology

The Office of Science and Technology (OST) produces regulations, guidelines, methods, standards, 

science-based criteria, and studies that are critical components of national programs that protect aquatic 

environments from the impacts of nutrient pollution. OST provides both technical and financial 

assistance to states to help them adopt numeric nutrient water quality standards. OST provides direct 

assistance to states by providing implementation guidance, addressing technical and policy issues that 

states raise, and providing technical information to support states rulemaking for standards. OST assists 

in building the scientific capacity for states through support for sampling and monitoring, training, data 

and statistical analysis, and modeling assistance for developing scientifically defensible nutrient criteria. 

OST also communicates the importance of managing nutrient pollution by integrating nutrient messages 

in communications and outreach products related to water quality standards.
76 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

I.D.3. Office of Research and Development

The mission of the Office of Research and Development is to conduct cutting-edge research and 

foster the sound use of science and technology to fulfill EPA’s statutory and regulatory requirements. Its 

research laboratories are structured along the risk paradigm by focusing research on exposure, effects, risk 

assessment and risk management. 

The National Exposure Research Laboratory

The National Exposure Research Laboratory (NERL) conducts research and development that leads to 

improved methods, measurements, and models to assess and predict exposures of humans and ecosystems 

to harmful pollutants and other conditions in air, water, soil, and food. NERL is conducting atmospheric 

deposition research and modeling of nitrogen, sulfur, and mercury as stressor inputs to water quality and 

ecosystem models to provide forecasts of changes in deposition due to management actions stemming 

from Clean Air Act regulations

The National Health and Environment Effects Research Laboratory

The National Health and Environment Effects Research Laboratory (NHEERL) conducts research to 

determine the impacts of environmental stressors on human and ecosystem health as well as the degree 

to which those stressors cause harm. NHEERL conducts research that improves the science supporting 

nutrient criteria development in estuaries and coastal waters. Case studies in Pensacola Bay, Florida, and 

Yaquina Bay, Oregon, have provided approaches that may be used to develop nutrient criteria and protect 

aquatic life. Additionally, NHEERL research on Gulf hypoxia is developing statistical, semi-empirical 

and coupled numerical model applications, data products, and other tools to quantify the biogeochemical 

processes and ecosystem responses to nutrient loads, quantify sources of uncertainty in nutrient 

load–hypoxia response relationships, and forecast the effects of nutrient management actions and load 

reduction targets on the extent of hypoxia. In situ observations and analyses from coastal and continental 

shelf cruises provide the empirical bases for the numerical simulation models of eutrophication and 

hypoxia on the continental shelf. Through an interagency agreement with the Naval Research Laboratory 

(NRL), a coupled water quality-sediment diagenesis model is being integrated into the NRL coastal ocean 

hydrodynamic model. The integrated numerical simulation model will provide improved mechanistic 

understanding of the processes regulating Gulf hypoxia. 

The National Center for Environment Assessment

The National Center for Environment Assessment develops new methods for risk assessment and 

applies those methods to the cutting-edge issues that the U.S. EPA faces. 

The National Risk Management Research Laboratory

The National Risk Management Research Laboratory (NRMRL) conducts research and technical 

assistance to provide the scientific basis to support the development of strategies and technologies 

to protect and restore ground water, surface water, and ecosystems impacted by man-made and 

natural processes. NRMRL conducts nutrient fate and transport modeling, incorporating surface 

water-groundwater interactions, in the Mississippi River Basin. It also conducts research to improve 

manure management practices and reduce impacts of manure runoff on water quality. In addition, the 

Laboratory’s research on best management practices focuses on evaluating how restoration techniques 

may enhance nutrient retention and attenuation in watersheds that are small enough for management 

practices to have a significant impact.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 77

Executive Summary Appendices

The National Center for Environmental Research

The National Center for Environmental Research (NCER) supports high-quality research that 

will provide the scientific bases for national environmental decisions. NCER supports cutting-edge, 

extramural research through competitions for grants, fellowships, and innovative small business research 

contracts. NCER’s Science to Achieve Results (STAR) Program funds research grants and graduate 

fellowships related to various aspects of hypoxia, including nutrient source, fate, and transport. Overall, 

STAR awards about 150 research grants and 125 graduate fellowships each year. NCER also makes 

awards under joint Request for Applications with partnering agencies. These grants and fellowships have 

been awarded to universities and nonprofit research institutions in all 50 states, Guam, Puerto Rico, and 

the District of Columbia.

Environmental Monitoring and Assessment Program

The Environmental Monitoring and Assessment Program (EMAP) is a research program to develop the 

tools necessary to monitor and assess the status and trends of national ecological resources. EMAP’s goal 

is to develop the scientific understanding for translating environmental monitoring data from multiple 

spatial and temporal scales into assessments of current ecological condition and forecasts of future risks 

to natural resources. The EMAP program also provides extramural funding through the STAR program. 

Through their Great Rivers Project, EMAP is providing an assessment of the ecological conditions in the 

Mississippi River Basin using a probability-based sampling design. This assessment will allow for statelevel assessment of those rivers within or adjacent to a state’s borders. 

National Environmental Scientific Computing Center and the Environmental Modeling and 

Visualization Laboratory 

The National Environmental Scientific Computing Center and the Environmental Modeling and 

Visualization Laboratory (EMVL) is an EPA-managed, contractor-operated facility designed to support 

EPA’s scientific modeling and large-scale data management research programs through the application 

of high performance computing and visualization tools. The mission of EMVL falls in two categories: 

1) to provide the high performance computing resources necessary to support environmental research of 

global proportions and improved science for the development of regulations and 2) to assist researchers 

in translating data into knowledge by using visual images to facilitate insight into that data. Currently, 

EMVL is supporting NHEERL research on Gulf hypoxia by assisting in the development of an integrated 

hydrodynamic, water quality, and sediment diagenesis simulation model for hypoxia in the Gulf of 

Mexico. 

I.E. Department of Interior

I.E.1. U.S. Geological Survey

Integrated Studies of Coastal Ecosystems

USGS conducts long-term assessments of the environmental and ecological conditions in aquatic 

ecosystems across the Nation in selected bays, estuaries, and other coastal environments. The research 

addresses a broad range of science issues related to environmental health and ecosystem management, 

including nutrient dynamics, algal blooms, and the role of terrestrial contributions of contaminants. The 

research in these ecosystems is coordinated closely with other Federal and local governmental agencies. 

Information about such programs are available at: 
78 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

San Francisco Bay: http://sfbay.wr.usgs.gov/access/wqdata/ 

Chesapeake Bay: http://chesapeake.usgs.gov/ 

Gulf of Mexico: http://toxics.usgs.gov/hypoxia/ 

Tampa Bay: http://gulfsci.usgs.gov/tampabay/ 

Galveston Bay: http://gulfsci.usgs.gov/galveston/ 

Boston Harbor: http://woodshole.er.usgs.gov/project-pages/bostonharbor/ 

Puget Sound: http://puget.usgs.gov/ 

National Streamflow Information Program 

The National Streamflow Information Program (http://water.usgs.gov/nsip) provides streamflow 

information at more than 7,000 stream gauges nationwide, funded by the USGS and over 800 local, state, 

and other Federal agencies, many of which represent downstream measuring sites for rivers discharging 

to the coast. These data are essential to understanding the role of and trends in freshwater contributions to 

coastal ecosystems and to quantifying the associated loadings of nutrients and other chemicals. 

Water Quality Monitoring

The USGS National Stream Quality Accounting Network measures the annual transport of nutrients, 

dissolved solids, selected pesticides, and suspended-sediment from selected large rivers to coastal 

waters of the United States and from major inland sub-basins for priority large rivers, where the source 

origins of chemical loads are needed to guide management actions. The network includes monitoring at 

approximately 18 major coastal rivers that contribute over 80 percent of the total discharge of streamflow, 

nitrogen, phosphorus, and suspended sediment to coastal waters of the United States. 

Nineteen additional stations within the Mississippi River Basin are monitored to define the source 

origins of streamflow and nutrients ultimately delivered to the Gulf of Mexico to guide management 

actions to mitigate hypoxia in the northern Gulf of Mexico. Other major river systems where chemical 

loads are monitored at inland stream sites to guide management actions include the Chesapeake Bay and 

San Francisco Bay watersheds. USGS water quality monitoring of flow and chemical delivery to coastal 

waters is used to make estimates of national coastal delivery, such as those developed by the Heinz Center 

(http://www.heinzctr.org/ecosystems/2002report/national/mvmt_n.shtml). 

The National Water Quality Assessment (NAWQA) (http://water.usgs.gov/nawqa/) Program conducts 

assessments of the quality of the Nation’s waters to provide an understanding of water quality conditions 

and how those conditions may vary locally, regionally, and nationally; whether conditions are getting 

better or worse over time; and how natural features and human activities affect those conditions. NAWQA 

Program scientists collect and interpret data about surface- and groundwater chemistry, hydrology, land 

use, stream habitat, and aquatic life in parts or all of nearly all 50 states using a nationally consistent study 

design and uniform methods of sampling analysis. Water quality monitoring for national status and trends 

provide important data on the occurrence and distribution of nutrients and other water quality constituents 

in representative basins throughout the Nation. These data are used to develop the SPARROW and other 

water quality models that provide significant knowledge of the source areas of nutrients and the human 

activities that affect nutrient loads. 

Groundwater Resources Program 

Freshwater delivered through groundwater discharge to coastal waters is essential to ecosystem 

function and coastal circulation, and can have a significant influence on the health of these ecosystems. 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 79

Executive Summary Appendices

The USGS Groundwater Resources Program (http://water.usgs.gov/ogw/gwrp) conducts studies along the 

Atlantic coast related to ground-water discharge and its role in coastal salinity balance and the role of the 

associated nutrient contributions in coastal hypoxia. Additional studies in these areas are conducted on a 

cooperative basis with local government agencies. 

Nutrient Dynamics and Biochemical Cycling in Wetland and Riverine Ecosystems

USGS conducts research to improve the understanding of the biogeochemical cycling of nutrients in 

riverine and wetland ecosystems. Ecosystem management of ecosystems is emerging as an effective 

means of protecting natural resources and reducing nutrient inputs to receiving waters. Effective 

ecosystem management requires knowledge of the biogeochemical cycling of nutrients (requiring analysis 

of internal and external sources and sinks of nutrients) and understanding of the processes that control 

these sources and sinks. In numerous aquatic ecosystems, many of these processes are poorly understood 

as are their potential interactions with other ecosystem properties, such as plant production. This research 

is being conducted primarily by the USGS National Research Program (http://water.usgs.gov/nrp), the 

NAWQA Program, the National Wetlands Research Center (http://www.nwrc.usgs.gov), and the Upper 

Midwest Environmental Science Center (http://www.umesc.usgs.gov).

I.F. National and Regional Interagency Efforts

I.F.1. Integrated Ocean Observing Systems

The U.S. Integrated Ocean Observing System (IOOS) (http://www.ocean.us) is a coordinated national 

network of observations and data transmission, data management, and communications intended to 

routinely and continuously acquire and disseminate quality controlled data and information on current and 

future states of the oceans and Great Lakes from the global scale of ocean basins to local scales of coastal 

ecosystems. The IOOS is part of the U.S. Integrated Earth Observing System, the U.S. contribution to the 

Global Ocean Observing System (http://www.ioc-goos.org), and a contribution to the international Global 

Earth Observation System of Systems.

I.F.2. National Monitoring Network and the National Water 

Quality Monitoring Council

In response for calls for a National Water Quality Monitoring Network for streamflow and the 

associated chemical delivery to coastal waters, the National Water Quality Monitoring Council (http://

acwi.gov/monitoring), a subgroup of the Advisory Committee on Water Information, was charged with 

designing this network. The design was developed by 80 representatives working through the National 

Water Quality Monitoring Council, including representatives from Federal, state, and local government 

organizations, universities, water associations, and the private sector. The Council is co-chaired by the 

USGS and the EPA, and its other Federal members include NOAA, Tennessee Valley Authority, USACE, 

USDA, and the remaining Department of the Interior (DOI) agencies. The Network will coordinate water 

quality monitoring across the Nation to provide a comprehensive database that supports assessment of the 

health of ocean, coastal, and Great Lakes resources. Additional information on the national monitoring 

network, including reports for the pilot phase conducted in three geographic areas (Delaware Bay, San 

Francisco Bay, and Lake Michigan) is available on at http://acwi.gov/monitoring/network.
80 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

I.F.3. National Estuary Program 

EPA’s National Estuary Program (NEP; http://www.epa.gov/owow/estuaries) is a national network 

of 28 programs working for collaborative solutions for estuaries designated by Congress as of critical 

importance. Created in 1987 under the Clean Water Act, the NEPs are charged with protecting and 

restoring U.S. estuaries by engaging state and Federal agencies, nongovernmental organizations, and 

local communities in planning and management. EPA provides base funding and Federal oversight for 

each of the NEPs, but program management is typically the responsibility of an estuary stakeholder-based 

management committee. 

Section 320 of the Clean Water Act (National Estuary Program) states that one of the main purposes of 

the NEP is to develop a comprehensive watershed ecosystem plan for the conservation and management 

of natural resources in NEP estuaries. NEPs are required to have inclusive stakeholder representation on 

any management or advisory committee. Representatives of state and Federal agencies (including EPA, 

USDA, and NOAA), interstate or regional agencies, local governments, industry and business, public and 

private educational institutions and the general public, should comprise such a committee.

I.F.4. Regional Efforts

Chesapeake Bay

The Chesapeake Bay Program (http://www.chesapeakebay.net) is a regional partnership charged 

with leading and directing restoration of the Chesapeake Bay. This partnership includes representatives 

from Maryland, Virginia, the District of Columbia, Pennsylvania, the Chesapeake Bay Commission, 

and citizen advisory groups. The Federal government is formally represented by the U.S. EPA, but a 

number of additional Federal partners are involved, including NOAA, USDA, National Park Service, 

USGS, USFWS, Federal Housing Administration, U.S. Coast Guard, National Aeronautics and Space 

Administration (NASA), U.S.Postal Service, General Services Administration, National Capital Planning 

Commission, Department of Defense, and Department of Education. Scientific guidance is provided by a 

Scientific Technical Advisory Committee. 

The Chesapeake Bay Program is leading efforts to improve water quality in the Bay, especially related 

to nutrients, with the goal of improving dissolved oxygen levels and habitat quality through working 

with farmers, developers, homeowners and local governments to reduce pollutants. In 1998, the EPA

and state members of the Bay Program (known as the Chesapeake Executive Council) signed the second 

Chesapeake Bay Agreement which called for a 40% reduction in nitrogen and phosphorus inputs by the 

year 2000. This nutrient reduction target was reaffirmed in 1992 and expanded to include Bay tributaries 

and a call for detailed tributary nutrient management strategies. A third agreement, Chesapeake 2000, 

also reaffirmed the 40% reduction target, but extended the target date to 2010 and outlined more specific 

strategies to meet the goal. 

Northern Gulf of Mexico

The Mississippi River/Gulf of Mexico Watershed Nutrient Task Force was formed in 1997 to 

understand the cause and effects of eutrophication in the Gulf of Mexico and to coordinate and support 

nutrient management activities within the Mississippi River Watershed. Members of the Task Force 

include executive level representatives from ten states, the EPA, NOAA, USACE, DOI, and USDA. 

Task Force members have designated senior managers within their respective agencies to serve on 

a Coordination Committee, which advises the Task Force on actions and manages workgroups and 

committees. In 2001, the Task Force released an “Action Plan” (Mississippi River/Gulf of Mexico 

Watershed Nutrient Task Force 2001) to address Gulf hypoxia and nutrient pollution within the watershed, 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 81

Executive Summary Appendices

setting a goal of reducing the annual size of the hypoxic zone to 5,000 km2 by 2015. Following a 

comprehensive scientific reassessment process that included an EPA Science Advisory Board Report 

(U.S. EPA 2007), the Task Force released a “2008 Action Plan” (Mississippi River/Gulf of Mexico 

Watershed Nutrient Task Force 2008) that reaffirmed the goal of 5,000 km2

, although it was recognized 

the 2015 target may not be met, and placed additional focus on the management of phosphorus in addition 

to nitrogen. To reach this goal, the “2008 Action Plan” (Mississippi River/Gulf of Mexico Watershed 

Nutrient Task Force 2008) also recommended nitrogen and phosphorus reductions of at least 45%. 

The Gulf of Mexico Alliance was formed in 2004 as a partnership between the five Gulf States 

(Florida, Alabama, Mississippi, Louisiana, and Texas) with the goal of increasing regional collaboration 

to protect and enhance the ecological and economic health of the Gulf. Although NOAA and EPA are 

designated as Federal coordinators, the Alliance actively partners with NSF, NASA, USACE, USDA, 

DOD, DOE, DOI, Department of Transportation, Department of Health and Human Services, and the 

Department of State. Following its formation, the Alliance released a three-year action plan in 2006 

(http://www.gulfofmexicoalliance.org) that identified reducing nutrient inputs as one of five priority 

issue areas. Under the priority, increasing regional coordination for the development of TMDL’s and 

addressing the hypoxic zone in the northern Gulf through an aligned Gulf States position were identified 

as key actions. Through its second action plan that began in 2009, the Alliance will continue to facilitate 

the development of coordinated nutrient criteria and reduce hypoxia in coastal waters and estuaries 

through increased coordination with Gulf Hypoxia Task Force and targeted watershed strategies.

Narragansett Bay

Significant cooperative efforts have been undertaken in Narragansett Bay to both understand and 

mitigate hypoxia. The Narragansett Bay Estuary Program (NBEP, http://www.nbep.org) was established 

in 1993 as part of the NEP. EPA, USDA, Rhode Island and Massachusetts state environmental agencies, 

academic partners (University of Rhode Island) and other nongovernmental stakeholders participate in 

the management of NBEP. The NBEP also works closely with other Federal partners including NOAA, 

USACE, USGS, and USFWS. Since 1998, scientists from the NBEP, along with volunteer scientists 

from academic institutions and state agencies, have been conducting monthly (or more often) dissolved 

oxygen surveys. The data from these surveys are available at: http://www.geo.brown.edu/georesearch/

insomniacs/links.html. A major menhaden fish kill in August 2003 was investigated by NBEP scientists 

in the context of the developing knowledge of dissolved oxygen dynamics in Narragansett Bay. The 

Rhode Island state legislature passed legislation the following year to reduce nitrogen inputs from 

wastewater treatment plants.

Great Lakes

In December 2004, the Great Lakes Regional Collaboration was launched as a result of a presidential 

executive order, creating a unique partnership of key members from Federal, state, and local governments, 

tribes, and other stakeholders for the purpose of developing a strategic action plan. The Federal 

members of the Task force are cabinet level secretaries of the Departments of State, Commerce, Defense, 

Agriculture, Housing and Urban Development, Transportation, and the Interior; EPA; and the Council 

on Environmental Quality. This strategic plan, the Great Lakes Regional Collaboration Strategy, was 

signed in December 2005 and is intended to build upon the extensive regional efforts to date, working 

together toward a common goal of restoring and protecting the Great Lakes ecosystem for this and future 

generations. Although hypoxia is not particularly emphasized, nutrient reduction is an important part of 

the strategy. http://www.glrc.us
82 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Puget Sound

A dramatic 2003 fish kill in Hood Canal which was caused by the temporary upwelling of hypoxic 

waters precipitated strong public and scientific interest in understanding hypoxia dynamics in the Puget 

Sound ecosystem. The goal of the Hood Canal Dissolved Oxygen Program (HCDOP) supported through 

Congressional funding to the University of Washington is to determine the sources of low dissolved 

oxygen in Hood Canal and its effect on marine life. HCDOP has worked with local, state, Federal, and 

tribal government policy makers to develop potential corrective actions that will restore and maintain a 

level of dissolved oxygen that will not stress marine life. HCDOP is a partnership of 28 organizations 

that conducts monitoring and analysis and develops potential corrective actions to address the low 

dissolved oxygen problem in Hood Canal, including Federal (NOAA, USGS, USFWS. USACE, EPA and 

U.S. Navy), state, and tribal entities. http://www.hoodcanal.washington.edu

In 2007, the state legislature created the Puget Sound Partnership which took over the role of the Puget 

Sound Action Team. The goals of the partnership are to prioritize cleanup and improvement projects; 

coordinate Federal, state, local, tribal, and private resources; encourage cooperation; and make decisions 

based on sound science—some of which will be provided by the HCDOP. Several Federal agencies are 

represented on the partnership councils, including NOAA, Navy, USGS, USFWS, and EPA. http://www.

psp.wa.gov

Long Island Sound

The Long Island Sound Study (LISS) was formed by EPA, the State of New York, and the State 

of Connecticut to cooperatively address the degraded ecosystem within Long Island Sound. This 

partnership also involves relevant nonprofit organizations, concerned citizens, as well as NOAA, EPA, 

USGS, USFWS, and USDA. The LISS completed a Comprehensive Conservation and Management 

Plan that identified hypoxia in the Sound as one of seven priority issues. To address hypoxia, in 1998 

the LISS adopted a 58.5% nutrient reduction target for nitrogen by 2014, and nutrient management plans 

for New York and Connecticut were formally approved by EPA in 2001. These nutrient management 

plans are focusing on both nonpoint and point source pollution. Scientific support for the management 

plan is developed through the LISS Scientific Technical Advisory Committee, with financial support 

provided through a cooperative agreement among the EPA and the New York and Connecticut Sea Grant 

Programs. The LISS also funds the monitoring of hypoxia, water quality, and plankton. http://www.

longislandsoundstudy.net
Scientific Assessment of Hypoxia in U.S. Coastal Waters 83

Executive Summary Appendices

Appendix II. Geographic Case Studies

Introduction and Background to Case Studies

The case studies presented here highlight selected coastal ecosystems that are geographically diverse 

and represent the spectrum of estuarine and coastal ocean ecosystems affected by hypoxia. The selected 

cases describe the range of circumstances, understanding, and scientific and management approaches 

across the United States (Figure A1). They provide examples of monitoring and research programs 

that have been or are being used to develop management plans. In some instances the outcomes of 

implemented management measures are also presented and should serve as encouragement that nutrientrelated dissolved oxygen problems can be improved with proper management. The exception is hypoxia 

along the Oregon coast, which has occurred since 2002 and is more related to climate impacts on 

upwelling-favorable winds on the west coast. Yet, coastal management is still pertinent to the Oregon 

shelf which has thriving coastal fisheries negatively impacted by hypoxia. These case studies provide the 

basis for successful management approaches that may be used in other systems in the United States. 

Figure A1. Geographic locations of hypoxia case studies. Large blue dots represent cases studies; red dots represent systems 

that have a documented hypoxia issue.
84 Scientific Assessment of Hypoxia in U.S. Coastal Waters

AppendicesSite Waterbody area (km2) Watershed area (km2) Average depth (m) Tidal height (m) Freshwater inflow

m3/d

Average salinity (psu)

Watershed population

NEEA Results*: Dissolved oxygen ratingEarly 1990s

Early 2000s

Long Island Sound 3,259 12,773 20 1.9 1.55 x 107 28 4.91 x 106 Moderate High

Lake Erie 25,744 --- 19 0 --- 0 --- --- ---Chesapeake Bay Mainstem 6,974 79584 7.3 0.45 1.05 x 108 16 6.41 x 106 High High

Pensacola Bay 477 17650 3.0 0.42 2.58 x 107 18 3.71 x 105 Moderate Low

Northern Gulf of Mexico 31,743 2,968,304 20 0.29 1.53 x 109 29 7.30 x 107 High High

Yaquina Bay 14 634 2.1 1.9 6.60 x 105 22 6.03x103 Low Low

Oregon Shelf 26,600 --- --- 3 - 4 (nearshore) 5.6 x 108 32 --- --- ---Hood Canal 396 2768 70 2.2 7.45 x 106 26 3.49 x 104 Moderate High

* from Bricker, S., B. Longstaff, W. Dennison, A. Jones, K. Boicourt, C. Wicks and J. Woerner. 2007. Effects of Nutrient Enrichment in the Nation’s Estuaries: A Decade of Change, National Estuarine Eutrophication Assessment Update. NOAA Coastal Ocean Program Decision Analysis Series No. 26. National Centers for Coastal Ocean Science, Silver Spring, MD. 322 pp. http://ccma.nos.noaa.gov/news/feature/Eutroupdate.html

Table A1. Comparison of Physical Systems Represented by Case Studies in Appendix II
Scientific Assessment of Hypoxia in U.S. Coastal Waters 85

Executive Summary Appendices

Long Island Sound

Physical Description of the System

Long Island Sound is a large (3,056 

km2) glacial outwash estuary, shared by 

the States of Connecticut and New York 

(Figure 1). Its unique configuration 

connects it with the Atlantic Ocean via the 

Race in the east and via the East River in 

the west. The Connecticut River, very near 

the Sound’s eastern terminus, contributes 

about two thirds of its freshwater input. 

The Housatonic and Thames Rivers also 

contribute significant volumes of fresh 

water to this system. The influence of 

the East River (a tidal strait) promotes a 

stratified salinity structure in the western 

sound especially in the spring runoff period 

when freshwater from the Hudson River basin is transported into western Long Island Sound. Salinity 

variability is less distinct in the eastern sound where salinities tend to be higher. Tidal amplitude ranges 

from about two meters in the west to less than one meter in the east. The Sound is moderately flushed, 

with mean residence times of two to three months. A highly developed watershed contributes to low 

dissolved oxygen problems (from Bricker et al. 1997, 2007).

History of Hypoxia (issue, causes, economic, and 

ecosystem impacts)

Long Island Sound has a large and highly developed watershed (Table A1). Nitrogen contributions 

from the watershed, combined with strong summer thermal stratification in its western half, renders Long 

Island Sound susceptible to seasonal hypoxia. Since 1985, the causes and effects of hypoxia have been 

the subject of intensive monitoring, modeling, and research through the Long Island Sound Study (LISS), 

part of the EPA National Estuary Program (see Appendix I, Interagency Efforts). Hypoxia most seriously 

affects the strongly stratified western half of the Sound where dissolved oxygen concentrations fall well 

below Connecticut and New York’s water quality standards each summer (Figure 2). Dissolved oxygen 

levels below 3 mg/L are usually 

observed, levels below 2 mg/L are not 

uncommon, and during some years 

portions of the Sound’s bottom waters 

become anoxic (<1 mg/L; Figures 2 

and 3). 

Long Island Sound is surrounded 

by a highly urbanized landscape, 

including New York City in the west 

and large, sprawling populated areas 

in Long Island and Connecticut. 

Primary sources of nitrogen include 

Figure 1. Location of Long Island Sound (P. Stacey, CT DEP).

Figure 2. The frequency and location of hypoxia in Long Island Sound bottom 

waters from 1991-2008 (P. Stacey CT DEP).
86 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

sewage treatment plants, nonpoint 

source runoff, and atmospheric 

deposition, all driven by human 

influences in the watershed and 

airshed (Figure 4). Monitoring 

of Long Island Sound conducted 

by the Connecticut Department 

of Environmental Protection on 

behalf of the LISS has shown an 

annual recurrence and persistence 

of hypoxia over the last 15 years. 

Despite significant reductions in 

nitrogen loads by both Connecticut 

and New York under a total 

maximum daily load (TMDL) 

approved in 2001, dissolved oxygen 

improvements have been slow 

and masked by weather-driven 

variability and effects of climate 

change.

Considering that nature contributes, at most, about 10,000 metric tons of nitrogen every year to 

the Sound from weathering and nitrogen fixation in the watershed, the nearly 38,000 metric tons per 

year added by more than 100 sewage treatment plants located along the coast and throughout the 

drainage basin have greatly enriched the ecosystem (Figure 5). Another 12,500 metric tons of nitrogen 

are contributed each year from nonpoint sources coming from excessive fertilizer added to lawns or 

agricultural crops, atmospheric emissions (from automobiles, power plants, and industry), and human and 

animal wastes (including home septic systems). Population continues to grow within the already densely 

populated Long Island Sound basin. This 

growth contributes to the nitrogen load 

through sewage treatment plants as well as

through various nonpoint sources, and the 

impact is large. Since 1985, Connecticut’s 

land conversion rate to developed uses 

was 11.3% for a population that had grown 

about 8.6%. Per capita consumption of 

land is outstripping population growth in 

Connecticut and throughout the basin.

Nitrogen enrichment, coupled with 

the Sound’s sensitivity to hypoxia 

due to relatively long residence time 

and seasonally strong stratification, 

leads to unhealthy conditions that are 

environmentally and economically costly 

for the Sound and its users. Furthermore, 

submerged aquatic vegetation (SAV) 

decline has been observed in many eastern 

Long Island Sound embayments and is 

Figure 3. Areal extent and duration of Long Island Sound hypoxia, 1987-2007. The 

average areal extent is 521 km2 and average duration is 58 days. (P. Stacey CT 

DEP).

Figure 4. Sources of nitrogen to Long Island Sound – baseline 

condition (P.Stacey, CT DEP).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 87

Executive Summary Appendices

believed to be linked to nitrogen enrichment. Nitrogen reductions to protect SAV will be much more 

stringent and difficult to attain than for low dissolved oxygen (Stacey 2007).

Science and Management Actions (to date and planned)

Since 1985, the causes and effects of hypoxia have been the subject of intensive monitoring, modeling, 

and research through the LISS. Through the Long Island Sound partnership, a dissolved oxygen 

TMDL was completed by Connecticut and New York and approved by U.S. EPA in 2001. Both states 

have aggressively pursued sewage treatment plant nitrogen control using biological processes, and 

nitrogen loads are trending downward. New York has relied upon traditional permitting programs to 

limit individual sewage treatment plants while Connecticut has instituted a statewide nitrogen trading 

program, called Nitrogen Credit Exchange, for 79 municipal sewage treatment plants (CT DEP 2007). 

The trading program works as an economic engine, forcing action towards the most cost-effective and 

environmentally beneficial projects. Collectively, the two states have accomplished a 30% reduction 

in sewage treatment plant nitrogen loads towards the TMDL target of 60–65% by 2014. The nitrogen 

trading program has proven to be a viable alternative for improving dissolved oxygen conditions in 

Long Island Sound and has accelerated the schedule to meet the TMDL wasteload allocation deadline. 

Potential savings with nitrogen trading are in the $200-400 million range over individual permitting 

approaches. The Nitrogen Credit Exchange could serve as a working model for incentive-based trading in 

other states.

Connecticut and New York are also relying on stormwater permitting and nonpoint source programs 

to meet a 10% reduction target for urban and agricultural lands. However, the nonpoint sources are 

more difficult and costly to control, especially atmospheric deposition, much of which originates from 

jurisdictions outside of Connecticut and New York. If attained, promised reductions from Federal 

Clean Air Act initiatives will help Long Island Sound tremendously. The LISS is also working with 

Massachusetts, New Hampshire, and Vermont, states that share the Long Island Sound watershed, to 

ascertain what level of reduction might be achieved in a cost-effective manner by those states. 

Figure 5. Estimated nitrogen loads to Long Island Sound, 1991-2004 (P. Stacey, CT DEP).
88 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Future Outlook

Population continues to grow within the already densely populated Long Island Sound basin. This 

growth contributes to the nitrogen load from sewage treatment plants as well as nonpoint sources. 

Despite the high land conversion rate since 1985, nitrogen loads have been reduced by some degree, 

largely through active management of sewage treatment. However, nutrient-related water quality 

problems have not improved as much as anticipated, in part, because of the high rate of per capita land 

consumption (sprawl) relative to population growth. As a result, management measures are offset by 

the increase in nutrient inputs related to population increases. In addition, the effects of climate change 

appear to have strengthened stratification in the Sound, exacerbating hypoxia.

References

Bricker S, Clement C, Frew S, Harmon M, Harris M, Pirhalla D. 1997. NOAA’s Estuarine Eutrophication Survey. 

Volume 2: Mid-Atlantic Region. Silver Spring, MD. Office of Ocean Resources Conservation Assessment. 51 pp.

Bricker S, Longstaff B, Dennison W, Jones A, Boicourt K, Wicks C, Woerner J. 2007. Effects of Nutrient Enrichment 

in the Nation’s Estuaries: A Decade of Change, National Estuarine Eutrophication Assessment Update. NOAA 

Coastal Ocean Program Decision Analysis Series No. 26. National Centers for Coastal Ocean Science, Silver 

Spring, MD. 322 pp. http://ccma.nos.noaa.gov/news/feature/Eutroupdate.html 

CT DEP. 2007. Connecticut’s Nitrogen Credit Exchange – An Incentive- based Water Quality Trading Program. The 

Connecticut Department of Environmental Protection, Bureau of Waer Protection and Land Reuse. Hartford, CT.

Stacey PE. Personal Communication. Connecticut Department of Environmental Protection.

Stacey PE. 2007. Long Island Sound, Ct & NY: Point source reductions lessened hypoxia in 1990s. In: Bricker S, 

Longstaff B, Dennison W, Jones A, Boicourt K, Wicks C, Woerner J. 2007. Effects of Nutrient Enrichment in the 

Nation’s Estuaries: A Decade of Change, National Estuarine Eutrophication Assessment Update. NOAA Coastal 

Ocean Program Decision Analysis Series No. 26. National Centers for Coastal Ocean Science, Silver Spring, MD. 

322 pp. http://ccma.nos.noaa.gov/news/feature/Eutroupdate.html 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 89

Executive Summary Appendices

Lake Erie

Physical Description of the System

Lake Erie is the shallowest of the Great Lakes with an average depth of 19 meters. It has three 

identifiable sub-basins: the eastern, central, and western basins. Lake Erie is deepest in the eastern basin 

and becomes increasingly shallow towards the west. Because it is the shallowest of the Great Lakes, 

it warms more quickly in the summer and cools more rapidly in the fall. The shallow depth and warm 

temperatures lead to high productivity. Thermal stratification, caused by warming of the upper layer, 

occurs throughout the Lake every summer. However, vulnerability to hypoxia is not consistent basin to 

basin. Eighty percent of the Lake’s water inflow comes from the Detroit River, but most of the nutrient 

and sediment loading comes from other tributaries, notably the Maumee River. Lake Erie receives the 

highest sediment loads of all the Great Lakes (Letterhos 2007).

History of Hypoxia (issue, causes, economic and 

ecosystem impacts)

The central basin of Lake Erie is the most vulnerable 

to hypoxia because it is sufficiently deep to develop 

thermal stratification, but the volume of water below the 

thermocline (or temperature gradient) is small enough 

that oxygen is depleted quickly. The water below the 

thermocline is cut off from oxygen in the surface water due 

to the stratification. The bottom waters in the central basin 

frequently go hypoxic during late summer through early 

fall (Charlton 1980, Rosa and Burns 1987). In contrast, the 

much deeper eastern basin, which also develops thermal 

stratification, has a much higher water volume below the 

thermocline, so the oxygen is not depleted before the water 

column mixes when the cold weather returns in the fall. 

The shallower western basin experiences stronger winddriven circulation that prevents stratification, and thus 

hypoxia, during most summers.

Although late summer hypoxia is a natural phenomena in Lake Erie probably dating back thousands 

of years (Delorme 1982), evidence suggests that the summer oxygen depletion rates increased during 

the 1950s and 1960s due to increased phosphorus loadings from point and nonpoint sources. Even the 

shallower western basin developed hypoxia during low wind periods (Hartman 1972, Leach and Nepszy 

1976, Beeton 1963). Concerted phosphorus reduction programs led to improved conditions until late 

1990s. However, the extent of bottom water hypoxia has returned to pre-action levels. The cause is much 

less clear, but likely related to increases in nutrient inputs from nonpoint sources (Richards, Unpublished 

Data) (Figure 1). Total phosphorous and soluble reactive phosphorous concentrations in the mainstem of 

the Lake have remained low, but levels in the nearshore areas are rising. Phosphorus, however, may no 

longer be the limiting nutrient; nitrogen and carbon may be playing greater roles (Letterhos 2007).

The effects of hypoxia on the Lake Erie ecosystem are not entirely clear. Some benthic species, 

such as burrowing mayflies (an important prey species), disappeared during periods of the most intense 

hypoxia (i.e., 1950s and 1980s) (Britt 1955, Carr and Hiltunen 1965, Krieger et al.1996). The loss of 

a thermal refuge due to low oxygen in the cooler bottom waters probably contributed to the decline of 

Figure 1. Hypoxia in Lake Erie in 2006. Source: 

IFYLE Program.
90 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

several commercially valuable benthic fishes (e.g., lake whitefish and burbot). The arrival of the zebra 

mussel in the 1980s caused tremendous ecological change and may be contributing to hypoxia. The 

effect on Lake Erie fisheries is currently an area of active research (see Appendix I, NOAA/GLERL 

International Field Years on Lake Erie).

Science and Management Actions (to date and planned)

The Great Lakes Water Quality Agreement of 1978 (http://www.epa.gov/glnpo/glwqa/1978/index.html) 

was a binational agreement between Canada and the United States which set strict limits on phosphorus 

loadings, a goal which was met in the 1980s (Hawley et al. 2006). The agreement targeted inputs from 

wastewater treatment plants, limited the use of phosphorus in detergents, and led to development of 

best management practices to reduce phosphorus from agricultural runoff. By the late 1980s, the goals 

outlined in the agreement were largely achieved and the incidence and extent of hypoxia significantly 

decreased (Hawley et al. 2006). However, the severity of hypoxia and levels of phosphorus in the lake 

began to increase in the 1990’s, although the cause is relatively unknown (Hawley et al. 2006).

In 1987 the governments of Canada and the United States also made a commitment, as part of the 

Great Lakes Water Quality Agreement, to develop a Lakewide Management Plan for the Great Lakes. 

The Lakewide Management Plan (LaMP) for Lake Erie (http://www.epa.gov/greatlakes/erie.html) is 

coordinated by Federal, state, and provincial government agencies in the two countries. Under the 

guidance of these agencies, the LaMP unites a network of stakeholders in actions to restore and protect 

the Lake Erie ecosystem. The LaMP provides an opportunity to link efforts to work toward the common 

goal of restoring Lake Erie for future generations.

In 2005, the International Field Years on Lake Erie (IFYLE) was initiated by researchers from the 

United States and Canada to conduct comprehensive research in the Lake, with an initial focus on hypoxia 

and harmful algal blooms. The primary objectives of this effort focus on quantifying the spatial extent 

of hypoxia to enable the development of forecasts as well as to determine the ecological consequences of 

hypoxia to Lake Erie living resources.

In December 2005, the Great Lakes Regional Collaboration (GLRC) released a Strategy to Restore and 

Protect the Great Lakes (http://www.glrc.us/strategy.html), which addressed nonpoint source pollution in 

the recommendations. More recently, the President’s 2010 Budget provided $475 million in EPA’s budget 

for a new Environmental Protection Agency-led, interagency Great Lakes Restoration Initiative. This 

Great Lakes Restoration Initiative is guided by the GLRC strategy and will target the most significant 

problems in the region, including invasive aquatic species, nonpoint source pollution, and contaminated 

sediment.

Future Outlook

The IFYLE will hopefully elucidate the most important factors contributing to the increase in hypoxia 

since the mid-1990s. Further, the impressive international cooperative effort in the region, represented 

by the Great Lakes Water Quality Agreement, LaMPs, Great Lakes Regional Collaboration (http://www.

glrc.us/), and the Great Lakes Restoration Initiative, to identify and reduce stressors in Lake Erie and the 

other Great Lakes improves the chance of reducing hypoxia in the future. Management actions that reduce 

nutrient loadings in Lake Erie may have positive ramifications for both freshwater harmful algal blooms 

and hypoxia.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 91

Executive Summary Appendices

References

Beeton AM. 1963. Limnological survey of Lake Erie in 1959 and 1960. Great Lakes Fishery Commission Technical 

Report 6: 1-32.

Britt NW. 1955. Stratification in western Lake Erie in summer of 1953: effects on the Hexagenia (Ephemeroptera) 

population. Ecology 36: 239-244.

Carr JF, Hiltunen K. 1965. Changes in the bottom fauna of western Lake Erie from 1930 to 1961. Limnology and 

Oceanography 10: 551-569.

Charlton MN. 1980. Oxygen depletion in Lake Erie: has there been any change? Canadian Journal of Fisheries and 

Aquatic Sciences 37: 72-81.

Delorme LD. 1982. Lake Erie oxygen: the prehistoric record. Canadian Journal of Fisheries and Aquatic Sciences 39: 

1021-1029.

Hartman WL. 1972. Lake Erie: effects of exploitation, environmental changes and new species on the fishery 

resources. Journal of the Fisheries Research Board of Canada 29: 899-912.

Hawley N, Johengen TH, Rao YR, Ruberg SA, Beletsky D, Ludsin SA, Eadie BJ, Schwab DJ, Croley TE, Brandt SB. 

2006. Lake Erie Hypoxia Prompts Canada-U.S. Study. EOS Transactions 87(32): 313-324.

Krieger KA, Schloesser DW, Manny BA, Trisler CE, Heady SE, Ciborowski JJH, Muth KM. 1996. Recovery of 

burrowing mayflies (Ephemeroptera: Ephemeridae: Hexagenia) in western Lake Erie. Journal of Great Lakes 

Research 22: 254-263.

Leach JH, Nepszy SJ. 1976. The fish community in Lake Erie. Journal of the Fisheries Research Board of Canada 

33: 622-638.

Letterhos J. 2007. Lake Erie Background from a Nutrient Perspective Prepared for the Ohio Phosphorus Task Force. 

Ohio EPA http://www.epa.state.oh.us/dsw/lakeerie/ptaskforce/LakeErieBackground.pdf 

Richards RP. Unpublished Data. Heidelberg University, Tiffin, Ohio.

Rosa F, Burns NM. 1987. Lake Erie central basin oxygen depletion changes from 1929-1980. Journal of Great Lakes 

Research 13: 684-696.
92 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Chesapeake Bay

Physical Description of the System 

The Chesapeake Bay is a drowned river valley that is almost 300 km long with a relatively deep (20-

30 m) and narrow (1-4 km) central channel (Kemp et al. 2005) (Figure 1). Broad shallow areas flank 

this central channel over its entire length (Boicourt et al. 1999), and the mean depth of the estuary is 6.5 

m (Kemp et al. 2005). Typically, the Bay is stratified with the surface freshwater isolating the deep and 

saline channel waters and limiting vertical mixing. Although 

occasionally strong wind events may cause some vertical 

exchange, stratification quickly returns due to the north-south 

salinity gradient (Boicourt 1992). There is a natural tendency 

for oxygen depletion in the deeper waters of the Bay due to the 

narrow and deep channel, persistent stratification, wide and 

shallow (and productive) sills flanking the channel, and a long 

water residence time (Boicourt 1992). 

Relative to other estuaries, the Chesapeake Bay watershed 

is large (172,000 km2

) compared to the size and volume of the 

estuary (Bricker et al. 1999). The shoreline is long (18,800 km) 

and many rivers drain the watershed into the Bay. The largest 

tributary is the Susquehanna River which accounts for 41% of the 

watershed. The Bay is closely connected to its watershed which 

delivers freshwater to the Bay at an average rate of 2,300 m3/s. 

Year-to-year fluctuations in river flow result in highly variable 

inputs of freshwater, nutrients, and sediment. The volume and 

nutrient composition of these flows influence stratification and 

productivity in the Bay (Kemp et al. 2005). This watershed is 

heavily populated, with an average density of 156 people per 

km2

. In addition to the major population centers surrounding 

and connecting Baltimore and Annapolis, Maryland; Washington 

D.C.; and Richmond, Virginia; agriculture is a prominent feature 

of the watershed’s landscape (Bricker et al. 2007).

History of Hypoxia (issue, causes, economic and 

ecosystem impacts)

A recent assessment of eutrophic conditions in the Bay showed that it is among the most impacted 

estuaries in the United States. Nitrogen loads are high, and the Bay is susceptible to development of 

nutrient-related problems (Bricker et al. 2007). Eutrophic symptoms occur periodically or persistently 

and over extensive areas. These symptoms include high concentrations of chlorophyll-a, hypoxia, loss 

of submerged aquatic vegetation, nuisance and toxic algal blooms, and excessive growth of macroalgae. 

Throughout the Bay and its tributaries, symptoms have either worsened or not changed between 1999 

and present (Bricker et al. 2007) (Figure 2). Primary sources of nutrients include agriculture, wastewater, 

and urban runoff. Other sources include septic tanks, sewer overflows, and atmospheric deposition. The 

sources of nutrient inputs and their transport have been described in detail by Boynton et al. (1995) who 

determined that nitrogen and phosphorus inputs from the watershed and atmosphere increased by six to 

eight fold and 13 to 24 fold, respectively, between pre-colonial times and the mid-1980s. About oneFigure 1. Dissolved oxygen conditions in the 

Chesapeake Bay in 2005

http://www.chesapeakebay.net/

bayforecastspring2006.htm 

www.eco-check.org
Scientific Assessment of Hypoxia in U.S. Coastal Waters 93

Executive Summary Appendices

fourth of the nitrogen and one-third of the phosphorus are from point sources, with the rest from nonpoint 

terrestrial and atmospheric sources (see Chapter 1, Figure 3). 

Several seasonally varying factors influence the dynamics of oxygen depletion from bottom-waters 

of the Bay. The decline in dissolved oxygen in the spring appears to be controlled primarily by physical 

processes (e.g., stratification). Whereas, the late spring decline and the extent of summer hypoxia appear 

to be influenced by the level of phytoplankton production and by water temperature (Hagy et al. 2004), 

both of which influence the respiration rate. On an annual basis, the amount of freshwater inflow is a 

good predictor of bottom-water oxygen depletion, because it controls water column stratification and, 

therefore, the rate of oxygen replenishment through vertical mixing. Freshwater runoff also delivers 

nutrients, which fertilize phytoplankton growth. Year-to-year variations in runoff have also been 

correlated with production and sedimentation of organic matter (Boynton and Kemp 2000) and increased 

dissolved oxygen demand. 

Evidence from sediment studies in the Chesapeake Bay suggests that hypoxia has increased in 

occurrence over many decades (Kemp et al. 2005). Geochemical and paleontological methods were used 

to interpret this indirect ecological history (Brush 1984), and results suggest that eutrophication increased 

starting in the 17th century, coinciding with settlement by Europeans. Eutrophication accelerated during 

the 20th century as indicated by a pronounced shift in the ratio of planktonic to, typically, benthic diatoms, 

reflecting a decline in both water clarity and benthic algal production (Cooper and Brush 1993). Increases 

in fossil abundance of hypoxia-tolerant species (Karlsen et al. 2000), iron pyrite (Cooper and Brush 1991, 

1993), and geochemical changes (Zimmerman and Canuel 2002) provide additional sedimentary evidence 

for development of hypoxia in the 20th century.

Figure 2. Volume of Chesapeake Bay affected by hypoxia/anoxia by year. 

http://www.chesapeakebay.net/bayforecastspring2006.htm

www.eco-check.org
94 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Year-to-year variations in hypoxia extent and intensity are correlated with the amount of nitrogen 

entering the Bay. The amount of hypoxia generated from a given level of nitrogen loading has, however, 

been more severe in recent years relative to the past (Hagy et al. 2004). Since the early 1990s, the volume 

of hypoxic water has increased, while nitrogen loading has leveled or declined (Boesch et al. 2001, 

Hagy et al. 2004, Langland et al. 2006)). In the mid-1980s, there was a shift in the relationship between 

hypoxia and nitrogen loading, suggesting that the Bay has passed an ecological threshold and is now more 

susceptible to eutrophication processes. This shift may have reduced the capacity of natural processes to 

both oxygenate the water column and trap nutrients in the sediments (Kemp et al. 2005). 

Further compounding the effects of eutrophication has been the dramatic loss of oyster beds (currently 

biomass is approximately 1% of the 19th century levels, Newell 1988). Oysters strongly influence the 

Bay ecosystems through an ability to assimilate nutrients and rebound from hypoxic events (Kemp et 

al. 2005). Oysters reduce concentrations of phytoplankton and other suspended particles through filterfeeding, thereby increasing light levels reaching the sediment (e.g., Cohen et al. 1984, Newell and Koch 

2004). The loss of oysters has reduced water clarity, which in turn has negatively impacted the growth 

of vital submerged aquatic vegetation. It has been estimated that at the height of ecosystem health, Bay 

waters were filtered once every four days, but the depleted filter feeder populations now require more than 

a year to filter the same volume (Newell 1988).

Although heavy fishing pressure and other stressors in Chesapeake Bay make it difficult to isolate 

effects of eutrophication on fish, an increased ratio of pelagic (water column-dwelling) to demersal 

(bottom-dwelling) fish species documented for the Chesapeake Bay (Kemp et al. 2005) is indicative of 

increased eutrophication. Some of the most noticeable changes were the increase in pelagic Atlantic 

Menhaden, and the decline in demersal blue crab and oyster landings. This shift from demersaldominated to pelagic-dominated fisheries has been observed for other coastal systems and is attributed, 

in part, to bottom-water hypoxia (e.g., Caddy 1993). It is not clear how hypoxia influences the habitat 

requirements of particular fish and invertebrates, but some species, such as sturgeons, can no longer 

reproduce or rear young in the Bay due to the lack of habitat with adequate oxygen and temperature levels 

(Niklitschek 2001, as cited in Kemp et al. 2005). 

Whereas impacts to fisheries have been difficult to determine, impacts of hypoxia on benthic animals 

have been well documented. The diversity, abundance, and productivity of many benthic animals is 

affected by seasonal hypoxia in the Bay, particularly in deeper water (Holland et al. 1987, Diaz and 

Rosenberg 1995), and the effective loss of habitat and fauna as a result of hypoxia can have profound 

effects on ecosystem energetics (Diaz and Rosenberg 2008). Estimates of biomass lost due to hypoxia are 

approximately 10,000 megatons of carbon per year, or 5% of the Bay’s total secondary production. Under 

healthy circumstances, an estimated 60% of benthic energy would be passed up the food chain in the Bay; 

therefore, it is estimated that hypoxic conditions in the Bay result in 6,000 megatons of carbon being lost 

as food energy for fisheries (Diaz and Rosenberg 2008). 

Science and Management Actions (to date and planned)

Eutrophication and its influence on hypoxia have been studied extensively in the Chesapeake Bay in 

an effort to produce information useful for effective management of water quality and critical habitats 

(Boesch et al. 2001, Kemp et al. 2005). For example, Bay research has demonstrated that nitrogen and 

phosphorus limitation for phytoplankton growth vary seasonally and regionally (Fisher et al. 1999, 

Malone et al. 1986), underscoring the need to regulate both nitrogen and phosphorus inputs to the Bay. 

In addition, studies in this system have shown that nitrogen removal from Chesapeake Bay through 

denitrification appears to be inhibited compared with estimates for other coastal ecosystems that do not 

experience seasonal hypoxia (Kemp et al. 1990). The Chesapeake Bay has also been subjected to long-
Scientific Assessment of Hypoxia in U.S. Coastal Waters 95

Executive Summary Appendices

term water quality monitoring, as well as a long-term benthic monitoring program that has been a key 

metric for assessing progress towards nutrient- and hypoxia-related goals. 

Historically, nutrient dynamics within the watershed have received less attention than in the Bay 

proper (Boesch et al. 2001), but there has recently been an increasing focus on the watershed processes. 

For example, it is clear that riparian zones, even in urban areas, are ‘hotspots’ of ecological function 

and can be effective at sequestering nutrients from runoff (Groffman et al. 2003). However, riparian 

zones can contribute to nitrogen loading in the Bay watershed when they undergo the “urban stream 

syndrome” (Groffman et al. 2004), which occurs where impermeable surfaces increase runoff leading to 

channel incision and lower water tables, thereby reducing denitrification potential in the watershed. This 

information has contributed to ongoing water quality improvement efforts. 

A reduction in eutrophication has been a top priority for management of the Chesapeake Bay in the 

last few decades (Boesch et al. 2001). Scientific research has improved public awareness and political 

interest in reversing eutrophication in the Chesapeake Bay (Malone et al. 1993), and a series of policies 

and adaptive management plans have evolved (Boesch et al. 2001). The Chesapeake Bay became the first 

estuary in the United States to be targeted by Congress for restoration and protection. An outgrowth of 

this recognition was the formation of a regional partnership of Bay states, the District of Columbia, and 

Federal agencies. An agreement to cooperatively work together to protect the Bay was codified in The 

Chesapeake Bay Agreement of 1983 (http://www.chesapeakebay.net/content/publications/cbp_12512.

pdf). This agreement was signed by what would become the Chesapeake Executive Council, a group 

comprised of the governors of Maryland, Virginia, and Pennsylvania; the mayor of the District of 

Columbia; the administrator of the EPA; and the chair of the Chesapeake Bay Commission. In support 

of this agreement and the Chesapeake Bay Program, a Scientific and Technical Advisory Committee was 

formed to provide the most recent and accurate information. In 1987, a second agreement was signed, 

pledging to reduce nitrogen and phosphorus inputs into the Bay by 40% by the year 2000. In 1992, 

amendments were added, reaffirming the original goals of the 1987 agreement, but also pledging the 

development of tributary-specific strategies to reduce nutrient inputs.

Recognizing a lack of progress towards restoration of the Bay, members of the Chesapeake Bay 

Program drafted and signed the Chesapeake 2000 Agreement (C2K; http://www.chesapeakebay.net/

content/publications/cbp_12081.pdf), which provided comprehensive and specific direction for improving 

the water quality in the Bay, particularly related to nutrients. Recognizing the need to address Bay water 

quality within the watershed, the governors of Delaware, New York, and West Virginia entered into 

an agreement with the Chesapeake Executive Council to meet the goals of the C2K. This agreement 

was more aggressive than the previous one and called for, based on 1985 levels, a 48% reduction in 

nitrogen and 53% in phosphorus inputs. In 2003 and 2004, 36 tributary strategies were completed that 

outlined specific measures for each tributary to reduce the inputs of nutrients into the Bay. A history of 

Chesapeake Bay eutrophication and the evolution of public policy and awareness are available in Boesch 

et al. (2001).

Even more recently, in May 2009, President Obama issued Executive Order 13508 on Chesapeake 

Bay Protection and Restoration. To bring the full weight of the federal government to address the 

Chesapeake’s challenges, the Executive Order established the Federal Leadership Committee (FLC) for 

the Chesapeake Bay, which is chaired by the Administrator of the U.S. Environmental Protection Agency 

and includes senior representatives from the departments of Agriculture, Commerce, Defense, Homeland 

Security, Interior and Transportation. The EO charged the FLC with developing and implementing a new 

strategy for protection and restoration of the Chesapeake region. One of the primary strategies of the EO 

is “to restore clean water” in the bay, with the specific goal of reducing nitrogen, phosphorus, sediment 
96 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

and other pollutants to meet Bay water quality goals for dissolved oxygen, clarity, chlorophyll-a and toxic 

contaminants (http://executiveorder.chesapeakebay.net/).

Research on nutrient cycling in soil-water systems of the Chesapeake Bay watershed provides 

fundamental insight into the movement of nutrients in agricultural systems and their impact on water 

resources. This research has led to the development of models for better predictions of nutrient transport 

via runoff as well as practical tools, such as the “Phosphorus Index” (adopted by all states in the Bay 

watershed), to guide nutrient management decisions on agricultural fields. The advent of Comprehensive 

Nutrient Management Planning has resulted in the development and implementation of best management 

practices (BMPs) for water and air quality protection. These BMPs range from traditional conservation 

practices—such as cover crops, riparian buffers, and constructed wetlands—to new technologies for 

precision application of fertilizers and manures to new practices for controlling and filtering drainage 

waters. Some of these BMPs can be transferred to nonagricultural uses, and ongoing research promises to 

deliver another generation of BMPs that immobilize nutrients and sediment.

A recent assessment of water quality trends in rivers feeding the Bay showed significant improvements 

in loadings of nitrogen (72% of sites showed downward trends), total phosphorus (81% of sites), and 

sediment (43% of sites), indicating that management actions are having some effect in reducing nutrients 

and sediments (Langland et al. 2006). However, to date, lower nutrient input has not improved dissolved 

oxygen levels overall in the Chesapeake Bay, although it has caused small-scale reversals in hypoxia 

(Diaz and Rosenburg 2008). Clearly, there are complex and poorly understood mechanisms that are 

acting to delay recovery of some ecosystem components (e.g., seagrass beds), and these mechanisms 

are priorities for scientific attention. Restoration of seagrass, oyster, and marsh habitats are expected to 

help the Bay’s recovery from eutrophication and hypoxia by priming key ecological processes that will 

enhance recovery through biological positive-feedback mechanisms (Kemp et al. 2005). 

Future Outlook 

Small improvements in dissolved oxygen conditions are expected for the mainstem of the Chesapeake 

Bay, and the outlook for rivers draining into the Bay ranges from slight deterioration to slight 

improvement (Bricker et al. 2007). This projection is an improvement from the last eutrophication 

outlook presented in 1999 (Bricker et al. 1999), when the Bay and its tributaries were expected to 

experience small to large levels of deterioration. These projections are based on the prediction of 

expected nutrient load increases from wastewater treatment, septic tanks, agriculture, and urban runoff.

Current potential management concerns include increasing nutrient loads from sources such as 

wastewater treatment, agriculture, urban runoff, atmospheric deposition, on-site septic tanks, and 

combined sewer overflow, particularly because an increase in population is expected in the watershed. To 

mitigate these potential problems, Bricker et al. (2007) suggests changes in land use policies that could 

limit urban sprawl and concentrate development, which could lead to more efficient treatment of runoff 

and waste. 

References

Boesch DF, Brinsfield RB, Magnien RE. 2001. Chesapeake Bay eutrophication: Scientific understanding, ecosystem 

restoration, and challenges for agriculture. J. Environ. Qual. 30: 303-320. 

Boicourt WC, Kuzmic M, Hopkins TS. 1999. The inland sea: circulation of Chesapeake Bay and the Northern Adriatic. 

In T. Malone, A. Malej, L. Harding, N. Smodlaka, R. Turner (eds.) Ecosystems at the land-sea margin: drainage 

basin to coastal sea. American Geophysical Union, Washington DC. P. 81-129.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 97

Executive Summary Appendices

Boicourt WC. 1992. Influences of circulation processes on dissolved oxygen in the Chesapeake Bay. In: Smith 

DE, Leffler M, Mackiernan G (eds.) Oxygen dynamics in the Chesapeake Bay: a synthesis of recent researchy. 

Maryland Sea Grant Publication, College Park, MD, p 7-59.

Boynton WR, Garber JH, Summers R, Kemp WM. 1995. Inputs, transformations, and transport of nitrogen and 

phosphorus in Chesapeake Bay and selected tributaries. Estuaries 18: 285-314. 

Boynton WR, Kemp WM. 2000. Influence of river flow and nutrient loading on selected ecosystem processes and 

properties in Chesapeake Bay. In: Hobbie J. (ed.) Estuarine science: a synthetic approach to research and 

practice. Island Press, Washington, DC, p. 269-298.

Bricker SB, Clement CG, Pirhalla DE, Orlando SP, Farrow DRG. 1999. National Estuarine Eutrophication 

Assessment: effects of nutrient enrichment in the nation’s estuaries. NOAA, National Ocean Service, Centers for 

Coastal Ocean Science, Silver Spring, MD. 

Bricker S, Longstaff B, Dennison W, Jones A, Boicourt K, Wicks C, Woerner J. 2007. Effects of nutrient enrichment 

in the Nation’s Estuaries: A decade of change. NOAA Coastal Ocean Program Decision Analysis Series No. 26. 

National Centers for Coastal Ocean Science, Silver Spring, MD. 322 pp.

Brush GS. 1984. Stratigraphic evidence of eutrophication in an estuary. Water Resour. Res. 20: 531-541.

Caddy JF. 1993. Toward a comparative evaluation of human impacts on fishery ecosystems of enclosed and 

semienclosed seas. Rev. Fish Sci 1: 57-95. 

Cohen RRH, Dresler PV, Philips EJP, Cory RL. 1984. The effect of the Asiatic clam Corbidula fulminea on 

phytoplankton of the Potomac River, Maryland. Limnol. Oceanogr. 29:170-18.

Cooper SR, Brush GS. 1991. Long-term history of Chesapeake Bay anoxia. Science 254:992-996. 

Cooper SR, Brush GS. 1993. A 2500-year history of anoxia and eutrophication in Chesapeake Bay. Estuaries 16: 

617-626.

Diaz RJ, Rosenberg R. 1995. Marine benthic hypoxia: a refvfiew of its ecological effects and the behavioral 

responses of benthic macrofauna. Oceanogr. Mar. Biol. Annu. Rev. 33:245-303.

Diaz RJ, Rosenberg R. 2008. Spreading dead zones and consequences for marine ecosystems. Science 321:926-

929.

Fisher TR, Gustafson AB, Sellner K, Lacuture R, Haas LW, Magnien R, Karrh R, Michael B. 1999. Spatial and 

temporal variation in resource limitation in Chesapeake Bay. Mar. Biol. 133: 763-778 

Hagy JD, Boynton WR, Keefe CW, Wood KV. 2004. Hypoxia in Chesapeake Bay, 1950-2001: Long-term change in 

relation to nutrient loading and river flow. Estuaries 27: 634-658.

Holland AF, Shaughnessy AT, Hiegel MH. 1987. Long-term variation in mesohaline Chesapeake Bay macrobenthos: 

spatial and temporal patterns. Estuaries 10: 227-245.

Groffman PM, Crawford MK. 2003. Denitrification potential in urban riparian zones. Journ. Environ. Qual. 32:1144-

1149.

Groffman PM, Law NL, Belt KT, Band LE, Fisher GT. 2004. Nitrogen fluxes and retention in urban watershed 

ecosystems. Ecosystems 7: 398-403.

Karlsen AW, Cronin TM, Ishman ES, Willard DA, Holmes CW, Marot M, Kerhin R. 2000. Historical trends in 

Chesapeake Bay dissolved osygen based on benthic Foraminifera from sediment cores. Estuaries 23: 488-508. 

Kemp WM, Sampou P, Caffrey J, Mayer M, Henriksen K, Boynton WR. 1990. Ammonium recycling versus 

denitrification in Chesapeake Bay sediments. Limnol. Oceanogr. 35: 1545-1536. 

Kemp WM, Boynton WR, Adolf JE, Boesch DF, Boicourt WC, Brush G, Cornwell JC, Fisher TR, Glibert PM, Hagy 

JD, Harding LW, Houde ED, Kimmel DG, Miller WD, Newell RIE, Roman MR, Smith EM, Stevenson JC. 2005. 

Eutrophication of Chesapeake Bay: Historical trends and ecological interactions. Mar. Ecol. Prog. Ser. 303: 1-29. 

Langland MJ, Raffensperger JP, Moyer DL, Landwehr JM, Schwarz GE. 2006. Changes in Streamflow and Water 

Quality in Selected Nontidal Basins in the Chesapeake Bay Watershed, 1985-2004. Scientific Investigations 

Report 2006–5178 U.S. Department of the Interior, U.S. Geological Survey. 74p. 
98 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Malone T, Kemp WM, Ducklow H, Boynton W, Tuttle J, Jonas R. 1986. Lateral variation in the production and fate of 

phytoplankton in a partially stratified estuary. Mar Ecol Prog Ser. 32: 149-160.

Malone T, Boynton W, Horton T, Stevenson C. 1993. Nutrient loading to surface waters: Chesapeake case study. In: 

Uman MF (ed.) Keeping pace with science and engineering. National Academy Press, Washington, DC p. 8-38. 

Newell RIE. 1988. Ecological changes in Chesapeake Bay: Are they the result of overharvesting the Eastern oyster 

(Crassostrea virginica)? In: Lynch MP, Krome EC (eds.) Understanding the estuary: advances in Chesapeake Bay 

research. Chesapeake Research Consortium Publication 129 (CBP/TRS 24/88) Bloucester Point, VA. pp. 536-

546.

Newell RIE, Koch EW. 2004. Modeling seagrass density and distribution in response tochanges in turbidity from 

bivalve filtration and seagrass sediment stabilization. Estuaries 27: 793-806. 

Niklitschek EJ. 2001. Bioenergetics modeling and assessment of suitable habitat for juvenile Atlantic and Shortnose 

stugeons (Acipenser oxyrinchus and A. brevirostrum) in the Chesapeake Bay. PhD. Dissertation, University of 

Maryland, College Park, MD.

Zimmerman AR, Canuel EA. 2002. Sediment geochemical records of eutrophication in the mesohaline Chesapeake 

Bay. Limn. Oceanogr. 47: 1084-1093.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 99

Executive Summary Appendices

Pensacola Bay

Physical Description of the System

The Pensacola Bay system is a network of 

estuarine bays located in the far western panhandle 

of Florida. The Bay system is arranged in two 

major arms that combine to form Pensacola Bay 

proper. The component bays include Escambia 

Bay, Blackwater Bay, East Bay, and Pensacola 

Bay (Figure 1). Santa Rosa Sound is relatively 

distinct shallow back-bay that joins the lower reach 

of Pensacola Bay and separates Santa Rosa Island 

from the mainland eastward to Destin, Florida, 

and Choctawhatchee Bay, Florida. The combined 

Pensacola Bay system, excluding Santa Rosa 

Sound, is medium sized (370 km2

) and shallow 

(mean depth is 3 m). Tides occur once per day 

and are relatively small, 15 to 65 centimeters. 

Three major watersheds drain into the Bay via the 

Escambia, Blackwater, and Yellow Rivers (Figure 

1).

History of Hypoxia (issue, 

causes, economic and ecosystem impacts)

The condition of the Pensacola Bay system, particularly that of Escambia Bay, became a matter of 

public concern as early as the late 1960s after significant industrial point source discharges began and 

extensive fish kills and hypoxia were observed (Olinger et al. 1975). The large fish kills prompted 

actions that ultimately led to elimination of the point source loadings by the mid-1970s. Olinger et al. 

(1975) provides a remarkable early compilation of ecological conditions in the Bay, intended principally 

to document the recovery of the system following reductions in industrial waste loads. These reports 

indicate that hypoxia was present in the Bays in the early 1970s, but does not provide enough data to 

evaluate the average extent or severity.

EPA monitored the Bay quarterly from 1996-2001 (U.S. EPA 2005) and monthly from 2002-

2004 (Hagy and Murrell 2007). Whereas differences in survey methodology and data reporting 

mostly preclude quantitative analysis of ecological changes since the early 1970s, comparison with 

the most recent data suggests that neither recovery nor further degradation has occurred. The major 

ecological concerns of the early 1970s continue: bottom water hypoxia, loss of seagrass habitats, toxic 

contamination, and degradation of biotic communities (Hagy et al. 2008).

Hypoxia occurs frequently and extensively in bottom waters of Pensacola Bay (Hagy and Murrell 

2007). An average of 25% of the Bay bottom is affected during the summer. Moderate river flow 

conditions create the highest potential for hypoxia in the Bay. In 2004, nearly 40% of the Bay bottom 

was hypoxic for two consecutive months (Hagy et al. 2008). Strong winds can bring hypoxic water onto 

shallow shoals, giving hypoxia the potential to degrade nearly all habitats in the Bay. Hypoxia has not 

been observed in the lower Bay, south and west of Bayou Texar, where tidal exchange with the Gulf of 

Mexico appears to be adequate to prevent hypoxia.

Figure 1. Map of Pensacola Bay, Florida.
100 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

The causes of hypoxia in Pensacola Bay include strong salinity stratification, low tidal mixing energy, 

and sluggish estuarine circulation, which create an optimal physical environment for hypoxia (Hagy 

and Murrell 2007). On the other hand, water clarity in the Bay is often relatively high, chlorophyll-a

concentrations are low to moderate, and phytoplankton production is moderate (Murrell et al. 2007). 

Correspondingly, rates of oxygen consumption in the water and sediments are relatively low (Murrell 

et al. 2009). These reflect low to moderate rates of nutrient loading, which can be related to low 

population density and minimal nutrient-intensive uses of much of the watershed (Hagy et al. 2008). The 

simultaneously low level of anthropogenic nutrient enrichment and eutrophication and high degree of 

hypoxia and seagrass loss suggests that the Bay has not been able to recover from earlier impacts.

The impact of hypoxia on biological communities in Pensacola Bay has not been well documented, 

but one can infer from the extent, frequency, and severity of hypoxia that affected habitats are almost 

certainly in a poor ecological condition. Limited data from the Florida Inshore Monitoring and 

Assessment Program show that the numbers of benthic macrofauna in Pensacola Bay in 2003 were 

only 5 to 10% of numbers in healthier regions of the Florida west coast. Livingston (1999) found that 

substantial biomass of infaunal animals occurred in only a narrow zone around the perimeter of the Bay, 

beyond the reach of persistent hypoxia. It has also been shown that chronic exposure to hypoxia imposed 

physiological stress on fish in Pensacola Bay, preventing them from reproducing (Thomas et al. 2007). 

Although the massive seagrass loss in Pensacola Bay has not been linked directly to hypoxia, it could 

reduce the abundance of animals that graze on algae growing on seagrasses, thus inhibiting their recovery. 

For example, grass shrimp enhanced growth of Ruppia maritima, a seagrass that was once abundant in 

Pensacola Bay (McCall and Rakocinski 2007). Conceivably, the massive loss of seagrasses that has 

occurred and the extensive recurrent hypoxia could be mutually reinforcing, promoting persistence of 

these conditions despite currently unremarkable rates of nutrient loading.

Science and Management Actions (to date and planned)

The record of scientific research addressing water quality and ecological condition in Pensacola Bay 

began in earnest with the Olinger et al. (1975) studies. These studies documented many of the key 

features of the ecology of the Bay, including the incidence of hypoxia and some of its physical causes. 

Papers by EPA scientists, mostly since 2000, provide more detail on many aspects of the physical and 

biological conditions that control hypoxia in the Bay (see Hagy et al. 2008). EPA will continue studies of 

Pensacola Bay as part of a regional research program in the northeast Gulf of Mexico. The project will 

focus on providing data and methods to develop numeric water quality criteria for nutrients and nutrientrelated water quality parameters.

Because Pensacola Bay is a relatively small estuary, no management programs have been created 

specifically to manage and improve its water quality (e.g., such as those created for Chesapeake Bay 

or the Gulf of Mexico). Florida’s Impaired Waters Rule provides some numeric guidelines for listing 

estuaries as impaired for chlorophyll-a and dissolved oxygen, but there are no enforceable water quality 

standards for nutrients or dissolved oxygen for the Bay. 

On the other hand, the state of Florida has recently increased its focus on developing water quality 

criteria for nutrients in its estuaries and coastal waters. Portions of Escambia Bay have been listed as 

impaired for an excessive increase in chlorophyll-a. Establishing levels for total maximum daily loads 

has been proposed and would call for significant reductions in both nitrogen and phosphorus loading to 

upper Escambia Bay. These actions signal an increase in regulatory attention to nutrients in Pensacola 

Bay. A continuation of scientific research by EPA and others could provide an improved scientific basis 

for these actions. Presently, the best hope for improved management of water quality in the Bay seems 

to be the likely prospect that the State of Florida will soon develop and adopt numeric nutrient criteria for 
Scientific Assessment of Hypoxia in U.S. Coastal Waters 101

Executive Summary Appendices

Pensacola Bay. EPA is collaborating with the Florida Department of Environmental Protection to support 

its efforts to achieve this objective for Pensacola Bay and other estuaries in Florida.

Future Outlook

The relatively undeveloped status of a large portion of the watershed of Pensacola Bay is one of its best 

assets. Arguably, low population density in the watershed has prevented eutrophication and hypoxia from 

becoming much worse. However, the population of the coastal counties surrounding the Bay, especially 

Santa Rosa County, Florida, is projected to grow nearly 3.5-fold by 2060 (Zwick and Carr 2006), most 

likely increasing nutrient loading to this sensitive system. A regulatory approach utilizing the authority 

of the Clean Water Act and based on numeric nutrient criteria will be the best way of ensuring that 

this growth occurs in a manner that does not further degrade the Bay. Although the available research 

clearly indicates that increased nutrients could harm water quality in the Bay, it is less clear that nutrient 

reductions alone will be sufficient to restore the Bay. A more active restoration program may be needed. 

Research is needed to determine the best methods for restoring ecological function in the Bay in order 

to simultaneously increase the extent of seagrass habitats, reduce hypoxia, and promote better biological 

condition overall. 

References

Hagy JD III, Murrell MC. 2007. Susceptibility of a Gulf of Mexico estuary to hypoxia: An analysis using box models. 

Estuarine, Coastal and Shelf Science. 74: 239-253

Hagy JD III, Kurtz JC, Greene RM. 2008. An approach for developing numeric nutrient criteria for a Gulf coast 

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

Environmental Effects Research Laboratory, Research Triangle Park, NC. EPA/600/R-08/004. 48 pp. 

Livingston RJ. 1999. Ecology and Trophic Organization, Section 5a, Volume 4 in Pensacola Bay System 

Environmental Study, unpublished report from Champpion International Corporation, 125 pp.

McCall DD, Rakocinski CF. 2007. Grass Shrimp (Palaemonetes spp.) play a pivotal trophic role inenhancing Ruppia 

maritima. Ecology 88(3): 618-624.

Murrell M C, Hagy JD III, Lores EM, Greene RM. 2007. Phytoplankton production in relation to nutrient distributions 

in a subtropical estuary: importance of freshwater flow. Estuaries and Coasts. 30(3): 390-402.

Murrell MC, Campbell JG, Hagy JD III, Caffrey J. 2009. Effects of irradiance on benthic and water column processes 

in a shallow micro-tidal estuary: Pensacola Bay, Florida, USA. Estuarine, Coastal and Shelf Science 81: 501-512.

Olinger LW, Rogers RG, Fore PL, Todd RL, Mullins BL, Bisterfield FT, Wise LA. 1975. Environmental and recovery 

studies of Escambia Bay and the Pensacola Bay system, Florida. Report No. 904/9-76-016, U.S. Environmental 

Protection Agency, Atlanta, Georgia. 468 pp.

Thomas P. Saydur Rahman M, Khan IA, Kummer JA. 2007. Widespread endocrine diisruption and reproductive 

impainment in an estuarine fish population exposed to seasonal hypoxia. Proceedings of the Royal Society B. 

274: 2693-2701.

U.S. EPA. 2005. The Ecological Condition of the Pensacola Bay System, Northwest Florida (1994-2001). U.S. 

Environmental Protection Agency, Office of Research and Development, National Health and Environmental 

Effects Research Laboratory, Gulf Ecology Division, Gulf Breeze, FL. EPA/620/R-05/002.

Zwick PD, Carr MH. 2006. Florida 2060, A population distribution scenario for the State of Florida. Geoplan Center, 

University of Florida, Gainsville, FL, USA. 29 pp.
102 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Northern Gulf of Mexico

Physical Description of the System

The largest zone of oxygen-depleted coastal waters in the United States and arguably the second 

largest on Earth is in the northern Gulf of Mexico on the Louisiana continental shelf (Figure 1). The 

Gulf hypoxic zone typically occurs in waters 5-60 m in depth up to 125 km offshore from west of the 

Mississippi River Delta and occasionally extending to the upper Texas coast. 

The dominant sources of freshwater, sediments, and nutrients to the northern Gulf of Mexico are 

the Mississippi and Atchafalaya Rivers. The watershed for these rivers (commonly referred to as the 

Mississippi Atchafalaya River Basin, or MARB) encompasses 41% of the contiguous United States 

(Figure 2). The average annual streamflow delivered from the MARB to the Gulf of Mexico during the 

period from 1981 to 2005 was 21,700 cubic meters per second (m3

/s); the average annual flux of total 

nitrogen and total phosphorus during that period was 1.47 and 0.14 million metric tons, respectively 

(Aulenbach et al. 2007). Streamflow from the MARB enters the Gulf of Mexico through two deltas—

about two thirds of the flow enters via the Mississippi River Birdfoot Delta (southeast of New Orleans, 

Louisiana), and one third via the Atchafalaya River Delta (200 km west on the central Louisiana coast). 

The freshwater discharge is carried predominantly westward along the Louisiana/Texas inner to midcontinental shelf, especially during peak spring discharge. This coastal ocean margin is characterized 

as a relatively shallow, open coastline with complex circulation patterns, weak tidal energies, generally 

high water temperatures, seasonally varying stratification strength, and large inputs of freshwater 

that effectively result in an unbounded estuary, stratified for much of the year. Water column density 

stratification, which is critical to bottom water oxygen depletion, is dominated by vertical salinity 

gradients, but thermal warming of surface waters intensifies summer stratification strength. Water 

column structure is also 

highly influenced by wind 

stress, frontal weather bands, 

hurricanes, and mixing of 

buoyant river plumes. 

History of 

Hypoxia 

(issue, causes, 

economic and 

ecosystem 

impacts)

Extensive bottom water 

hypoxia forms each year between May and September. Since 1985 (when systematic mapping was 

started), the hypoxic area has averaged 13,808 km2 and achieved its maximum size in 2002 at 22,000 

km2 (Figure 3). While low dissolved oxygen is commonly considered a bottom-water condition, 

oxygen-depleted waters often extend up into the lower half to two-thirds of the water column. Longterm increases in nutrient loads from the MARB, coupled with water column stratification, have been 

implicated as the primary causes of hypoxia (CENR 2000, U.S. EPA 2007). However, the complex 

physical, chemical, and biological processes along the coastal ocean margin—which consume, transform, 

and remineralize riverine nutrients and organic matter and ultimately result in bottom water oxygen 

depletion—remain poorly resolved in space and time.

Figure 1. Map of bottom water oxygen levels in mg/L. Black line is less then 2 mg/L

(hypoxic). 

Data source: N. Rabalais, Louisiana Universities Marine Consortium, NOAA, map by B. 

Babin.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 103

Executive Summary Appendices

The nutrients delivered with 

freshwater inputs support primary 

productivity within the immediate 

vicinity of the river discharges as well 

as across the broader continental shelf. 

The settling of fixed carbon to the lower 

water column and seabed in the form of 

senescent phytoplankton, zooplankton 

fecal pellets, or aggregates provides a 

large carbon source for decomposition 

by aerobic bacteria, which in turn leads 

to hypoxia. Tropical storms, hurricanes, 

and cold front passages disrupt the 

hypoxia until stratification reestablishes 

and oxygen depletion processes continue.

Low oxygen events on the LouisianaTexas continental shelf have been 

reconstructed over the past centuries 

using the relative abundance of low 

oxygen tolerant benthic foraminifera in 

sediment cores (Osterman et al. 2005). These records show that low oxygen events have increased over 

the past 50 years. Additionally, regression model hindcasts using historical Mississippi River discharge 

and nitrate concentrations indicated that large-scale hypoxia has likely been present along the continental 

shelf since the mid-1950s (Greene et al. 2009). More recently, the areal extent of the hypoxic zone 

increased from an average of 6,900 km2

 during 1985-1992 to 15,570 km2 during 2005-2009 (Rabalais and 

Turner 2006, LUMCON 2009) (Figure 3). 

The increased prevalence of Gulf hypoxia over recent decades has been related to increases in nutrient 

loads (CENR 2000, U.S. EPA 2007). However, it has been demonstrated that hypoxia events have 

occurred for centuries driven by high streamflow events that flush nutrients from wetland ecosystems and 

stratify ocean waters (Osterman et al. 2005, Swarzenski et al. 2008). Alterations of the Mississippi and 

Atchafalaya Rivers for transportation and flood control over two centuries have significantly lessened 

the assimilation of nutrients in the watershed and changed the pattern of freshwater discharge to the 

coastal ocean margin (U.S. EPA 2007). Concurrent increases in anthropogenic inputs of nutrients to the 

watershed have contributed to increased eutrophication and hypoxia (from Bricker et al. 1998, Rabalais in 

Bricker et al. 2007). 

The region supports some of the most valuable commercial and recreational fisheries in the United 

States (Diaz and Solow 1999, Chesney et al. 2000, Zimmerman and Nance 2001). For example, Texas 

and Louisiana lead all states in catches of shrimp, which is the largest U.S. commercial fishery (NOAA

2007). However, partitioning the impacts of hypoxia on living resources from other ecosystem stressors 

(e.g., climate change and overfishing) has proven difficult and significant knowledge gaps remain. Fish 

kills are occasionally reported and significant impacts to benthic fauna have been well documented (e.g., 

Rabalais et al. 2001). Zimmerman and Nance (2001) suggest that severe hypoxic conditions may block 

the migration of shrimp from nearshore to offshore habitats. Additionally, brown shrimp are subjected 

to a significant amount of habitat loss due to hypoxia (Craig et al. 2005), congregating in suboptimal 

environments along the hypoxic zone edge, possibly causing a reduction in growth (Craig and Crowder 

2005). Recent advancements in biomarker techniques have suggested that hypoxia may be causing 

Figure 2 Mississippi River Watershed with Dead Zone shown in Red 

(modified from Mississippi River/Gulf of Mexico Watershed Nutrient Task Force 

2004).
104 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

reproductive impacts in 

croaker as well (Thomas et 

al. 2007). 

Science and 

Management 

Actions (to 

date and 

planned)

In 1998, the EPA 

established the Mississippi 

River/Gulf of Mexico 

Watershed Nutrient Task 

Force. The Task Force 

brought together Federal 

agencies, states, and tribes 

to consider options for reducing, mitigating, and controlling hypoxia in the northern Gulf of Mexico. 

In 1999 and 2000, the results of an integrated science assessment, requested by the Task Force and 

conducted under the auspices of the National Science and Technology Council, was published (CENR 

2000, Brezonik et al. 1999, Diaz and Solow 1999, Doering et al. 1999, Goolsby et al. 1999, Mitsch et al. 

1999, and Rabalais et al. 1999) (http://oceanservice.noaa.gov/products/pubs_hypox.html). Using this 

science assessment, the Task Force published its first “Action Plan”, entitled Action Plan for Reducing, 

Mitigating, and Controlling Hypoxia in the Northern Gulf of Mexico (Mississippi River/Gulf of Mexico 

Watershed Nutrient Task Force 2001), which was endorsed by Federal agencies, states, and tribal 

governments. The 2001 Action Plan coastal goal was to reduce the five-year running average size of the 

hypoxic zone to 5,000 km2 by 2015 (Figure 3). It estimated that an overall reduction in nitrogen load of 

30–45% would be required. The 2008 Plan identifies the requirement that phosphorus as well as nitrogen 

loads be reduced and increases the required reduction to at least 45%. The 2008 Plan also notes that 

reductions in nitrogen loads from 2001-2005 were from nitrogen forms other than nitrate, which is the 

primary form fueling spring primary production that leads to hypoxia. The Action Plan was based on a 

series of voluntary and incentive-based activities that address both reducing nutrient inputs and increasing 

assimilation in aquatic ecosystems, including proper timing and amount of fertilizer applications, best 

management practices on agricultural lands, restoration and creation of wetlands, river hydrology 

remediation, riparian buffer strips, nutrient removal from stormwater and wastewater, and coastal 

diversions. 

In 2007, an updated science assessment was conducted by the EPA Science Advisory Board under 

the oversight of the Task Force (U.S. EPA 2007). This update science assessment was used by the Task 

Force to develop the Gulf Hypoxia Action Plan for Reducing, Mitigating, and Controlling Hypoxia in 

the Northern Gulf of Mexico and Improving Water Quality in the Mississippi River Basin (Mississippi 

River/ Gulf of Mexico Watershed Nutrient Task Force 2008) (see Box 4 in Chapter 2). This plan 

retains the coastal goal of reducing the hypoxic zone to less than 5,000 km2 by 2015, but understands 

the difficulty of meeting the goal. In this regard, the Task Force accepts the advice of the EPA Science 

Advisory Board on this issue: “The 5,000 km2

 target remains a reasonable endpoint for continued use in 

an adaptive management context; however, it may no longer be possible to achieve this goal by 2015... it 

is even more important to proceed in a directionally correct fashion to manage factors affecting hypoxia 

than to wait for greater precision in setting the goal for the size of the zone. Much can be learned by 

Figure 3. Northern Gulf of Mexico hypoxic area by year, including 5 year running and longterm averages. Action Plan Goal is 5000 km2

.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 105

Executive Summary Appendices

implementing management plans, documenting practices, and measuring their effects with appropriate 

monitoring programs” (U.S. EPA 2007). The 2008 Action Plan, also like the 2001 Action Plan, calls for a 

reassessment after five years. The next reassessment will be conducted in 2013.

On June 16, 2010, USDA released a report, “Effects of Conservation Practices on Cultivated Cropland 

in the Upper Mississippi River Basin.”(http://www.nrcs.usda.gov/technical/nri/ceap/umrb/index.html) 

This report, part of USDA’s Conservation Effects Assessment Project (CEAP), showed that agricultural 

producers in the Upper Mississippi River Basin have had great success in reducing soil erosion through 

widespread adoption of sediment controlling conservation activities. The assessment also showed 

that more widespread adoption of effective nutrient control practices is needed to meet the challenges 

associated with nitrogen and phosphorous leaching and runoff. USDA has committed $320 million to 

improve water quality in priority watersheds through its Mississippi River Basin Healthy Watersheds 

Initiative (MRBI).

Future Outlook

Although overall total annual nutrient loads to the northern Gulf from 2001–2005 suggests a decline 

in nitrogen inputs relative to the previous 24-year average (Mississippi River/Gulf of Mexico Watershed 

Nutrient Task Force 2008), reductions in nitrate during the critical spring period have not occurred. 

Further, the five-year running average (2005–2009) of the hypoxic zone is 15,570 km2, which is more 

than three times the Action Plan goal of 5,000 km2. The adaptive management approach put forth in 

the Action Plans of 2008 and 2001 commits to a reliance on sound science and continual feedback 

between the interpretation of new information and improved management actions as the key to targeting 

actions within watersheds where they will be most effective. Significant variability in nutrient export 

rates, hypoxic zone size, and other parameters resulting from anthropogenic and/or climate change will 

make it difficult to assess the outcome of nutrient management actions. However, targeted monitoring 

on representative watersheds, continued monitoring of streamflow and nutrient flux, and research that 

addresses biogeochemical processes and improved model application will provide the most effective 

means of measuring results and providing feedback on performance.

References

Aulenbach BT, Buxton HT, Battaglin WA, Coupe RH. 2007. Streamflow and nutrient fluxes of the MississippiAtchafalaya River Basin and subbasins for the period of record through 2005: U.S. Geological Survey Open-File 

Report 2007-1080.

http://toxics.usgs.gov/pubs/of-2007-1080/index.html

Brezonik PL, Bierman VJ, Alexander R, Anderson J, Barko J, Dortch M, Hatch L, Hitchcock GL, Keeney D, Mulla D, 

Smith V, Walker C, Whitledge T, Wiseman WJ. 1999. Effects of reducing nutrient loads to surface waters within the 

Mississippi River Basin and Gulf of Mexico. Topic 4 Report for the Integrated Assessment on Hypoxia in the Gulf of 

Mexico. NOAA Coastal Ocean Program Decision Analysis Series No. 18. Silver Spring, MD: National Oceanic and 

Atmospheric Administration. 

Bricker S, Clement C, Frew S, Harmon M, Harris M, Pirhalla D. 1998. NOAA’s Estuarine Eutrophication Survey. 

Volume 4: Gulf of Mexico Region. Silver Spring, MD. Office of Ocean Resources Conservation Assessment. 78 pp.

CENR (Committee on Environment and Natural Resources). 2000. Integrated Assessment of Hypoxia in the Northern 

Gulf of Mexico. National Science and Technology Council Committee on Environment and Natural Resources, 

Washington, D.C.

Chesney EJ, DM Baltz, RG Thomas. 2000. Louisiana estuarine and coastal fisheries and habitats: perspectives from 

a fish’s eye view. Ecological Applications 10: 350-366.

Craig JK, Crowder LB. 2005. Hypoxia-induced habitat shifts and energetic consequences in Atlantic croaker and 
106 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

brown shrimp on the Gulf of Mexico shelf. Mar. Ecol. Prog. Ser. 294:79-94.

Craig JK, Crowder LB, Henwood TA. 2005. Spatial distribution of brown shrimp(Farfantepenaeus aztecus) on the 

northwestern Gulf of Mexico shelf: effects of abundance and hypoxia. Canadian Journal of Aquatic Science 

62:1295-1308.

Diaz RJ, Solow A. 1999. Ecological and economic consequences of hypoxia—Topic 2, Gulf of Mexico hypoxia 

assessment: Silver Spring, MD, NOAA Coastal Ocean Program Decision Analysis Series, 86 pp., http://

oceanservice.noaa.gov/products/hypox_t2final.pdf 

Doering OC, Diaz-Hermelo F, Howard C, Heimlich R, Hitzhusen F, Kazmierczak R, Lee J, Libby L, Milon W, Prato T, 

Ribaudo M. 1999. Evaluation of economic costs and benefits of methods for reducing nutrient loads to the Gulf 

of Mexico. Topic 6 Report for the Integrated Assessment on Hypoxia in the Gulf of Mexico. NOAA Coastal Ocean 

Program Decision Analysis Series No. 20. Silver Spring, MD: National Oceanic and Atmospheric Administration. 

Goolsby DA, Battaglin WA, Lawrence GB, Artz RS, Aulenbach BT, Hooper RP, Keeney DR, Stensland GS. 1999. 

Flux and sources of nutrients in the Mississippi-Atchafalaya River Basin. Topic 3 Report for the Integrated 

Assessment on Hypoxia in the Gulf of Mexico. NOAA Coastal Ocean Program Decision Analysis Series No. 17. 

Silver Spring, MD: National Oceanic and Atmospheric Administration. 

Greene RM, Lehrter JC, Hagy JD III. 2009. Multiple regression models for hindcasting and forecasting midsummer 

hypoxia in the Gulf of Mexico. Ecological Applications 19(5): 1161-1175.

LUMCON. 2009. ‘Dead Zone’ again rivals record size: Press Release, Louisianna Universities Marine Consortium 

(LUMCON), http://www.gulfhypoxia.net/research/shelfwidecruises/2008/PressRelease08.pdf

Mississippi River/Gulf of Mexico Watershed Nutrient Task Force. 2001. Action Plan for Reducing, Mitigating, 

and Controlling Hypoxia in the Northern Gulf of Mexico. Washington, D.C.: Offices of Wetlands, Oceans, and 

Watersheds, U.S. Environmental Protection Agency.

Mississippi River/Gulf of Mexico Watershed Nutrient Task Force. 2004. A Science strategy to support management 

decisions related to hypoxia in the Northern Gulf of Mexico and excess nutrients in the Mississippi River Basin: 

Prepared by the Monitoring Modeling and Research Workgroup of the Mississippi River/Gulf of Mexico Watershed 

Nutrient Task Force, U.S. Geological Survey Circular 1270, 58 pp. 

Mississippi River/Gulf of Mexico Watershed Nutrient Task Force. 2008. Gulf Hypoxia Action Plan 2008 for Reducing, 

Mitigating, and Controlling Hypoxia in the Northern Gulf of Mexico and Improving Water Quality in the Mississippi 

River Basin. Washington, D.C.

Mitsch WJ, Day JW, Gilliam JW, Groffman PM, Hey DL, Randall GW, Wang N. 1999. Reducing nutrient loads, 

especially nitrate-nitrogen, to surface water, ground water, and the Gulf of Mexico. Topic 5 Report for the 

Integrated Assessment on Hypoxia in the Gulf of Mexico. NOAA Coastal Ocean Program Decision Analysis Series 

No. 19. Silver Spring, MD: National Oceanic and Atmospheric Administration.

NOAA. 2007. Nutrient Enhanced Coastal Ocean Productivity (NECOP) Program: National Oceanic and Atmospheric 

Administration, Washington, DC. http://www.aoml.noaa.gov/ocd/necop

Osterman LE, Poore RZ, Swarzenski PW, Turner RE. 2005. Reconstructing a180-yr record of natural and 

anthropogenic induced hypoxia from the sediments of the Louisiana continental shelf: Geology 33(4): 329–332.

Rabalais NN, Turner RE, Justic D, Dortch Q, Wiseman WJ. 1999. Characterization of hypoxia. Topic 2 Report for the 

Integrated Assessment on Hypoxia in the Gulf of Mexico. NOAA Coastal Ocean Program Decision Analysis Series 

No. 15. Silver Spring, MD: National Oceanic and Atmospheric Administration. 

Rabalais NN, Harper DE Jr., Turner RE. 2001. Response of nekton and demersal and benthic fauna to decreasing 

oxygen concentrations, p. 115-128. In: NN Rabalais and RE Turner (eds), Coastal Hypoxia Consequences for 

Living Resources and Ecosystems. Coastal and Estuarine Studies 58, American Geophysical Union, Washington 

D.C.

Rabalais NN, Turner RE. 2006. Oxygen depletion in the Gulf of Mexico adjacent to the Mississippi River, in Neretin, 

L.N., ed., Past and present marine water column anoxia: NATO Science Series, IV-Earth and Environmental 

Sciences, Kluwer, pp. 225–245.

Swarzenski PW, Campbell PL, Osterman LE, Poore RZ. 2008. A 1000-year sediment record of recurring hypoxia off 

the Mississippi River: the potnetial role of terrestrially-derived organic matter inputs. Marine Chemistry 109: 130-

142.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 107

Executive Summary Appendices

Thomas P, Rahman MS, Khan IA, Kummer JA. 2007. Widespread endocrine disruption and reproductive impairment 

in an estuarine fish population exposed to seasonal hypoxia. Proc. Royal Society B-Biological Sciences 274: 

2693-2702.

U.S. EPA. 2007. Hypoxia in the Northern Gulf of Mexico: An Update by the EPA Science Advisory Board: EPA-SAB08-004, December 2007, Washington, D.C., 275 pp.

Zimmerman AR, Nance JM. 2001, Effects of hypoxia on the shrimp industry of Louisiana and Texas, In Rabalais, 

NN, Turner RE (eds.), Coastal hypoxia—Consequences for living resources coastal and estuarine studies: 

Washington, D.C., American Geophysical Union, chap. 15, v. 58, pp. 293–310.
108 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Northeast Pacific Continental Shelf 

(Oregon/Washington)

Physical Description of the 

System

The Oregon and Washington Shelf out to 200 meters 

water depth encompasses approximately 26,600 

square kilometers (km2) and has an average width of 

approximately 40 km. Generally, the shelf narrows 

from north to south, with a shelf width of more than 60 

km off Washington and less than 20 km along southern 

Oregon. The exception to this general trend is a region 

called Heceta Bank in the central region of Oregon 

(43.8° to 44.6° N) which extends out to 65 km.

The shelf is part of the Northern California Current 

system. This system has strong seasonal variability, 

with northerly (from the north) winds dominating from 

April to October, and southerly winds dominating 

through the winter. The strong northerly winds induce 

coastal upwelling which brings nutrient-rich, lowoxygen waters onto the shelf (Figure 1).

The major source of terrestrial input to the system is 

from the Columbia River, with an annual mean outflow of 6484 cubic meters per second (m3

/s, 15 year 

mean from 1992 – 2006). River outflow tends to be low during the summer growing season and the 

input of nutrients from the river is negligible compared to contributions from upwelled waters (Hickey 

and Banas 2003). Thus, hypoxia off Washington and Oregon is unique in that it is due to natural sources 

rather than anthropogenic sources. 

Economically, upwelling-induced productivity in Oregon-Washington Shelf waters supports a 

$50 million fishery for dungeness crabs. This is a pot fishery, so crabs trapped in the pot fishing gear are 

killed during summertime hypoxic events. The value 

of the salmon fishery is on the order of $10-20 million; 

however, the impact of hypoxia on the landings of 

the crabs and salmon has not yet been evaluated 

economically. 

History of Hypoxia (issue, 

causes, economic and 

ecosystem impacts)

Evidence of hypoxia on the Oregon-Washington 

continental shelf indicates that it is a seasonal 

occurrence (Figure 1) that has been present since at 

least the 1960s (Figure 2). However, there has not 

been a consistent sampling program developed to 

Figure 1. Seasonal change in bottom water oxygen 

concentration at a station 5 miles from shore off Newport, OR. 

The horizontal line at 1.4 ml/L represents hypoxic waters. Note 

that hypoxic waters appear only during the upwelling season 

(May-October). Source: Bill Peterson, NOAA NWFSC.

Figure 2. Oxygen concentration (ml/L) within 10m of the 

bottom at a station 5 miles offshore of Newport, OR. The 

thick, red line indicates hypoxic waters (1.4 ml/L). Although 

hypoxia was observed in the 1960s, it has been observed 

more frequently in this century. Source: Bill Peterson, 

NOAA NWFSC.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 109

Executive Summary Appendices

assess the degree and magnitude of hypoxia over time (note the lack of any data between 1970 and 1998 

in Figure 2). Data have been collected three to four times per year since 1998 during broad-scale surveys 

of zooplankton and salmon and biweekly since late 2005 (Figure 1). 

Cross-shelf transects (Figure 3) show that the hypoxic bottom waters can extend at least 20 

to 30 meters off the bottom and occupy up to 30% of the water column. Low oxygen water 

moves onto the shelf in early spring (April or May) during the onset of upwelling. Throughout the 

summer, the oxygen level of bottom waters is reduced through the biological degradation of organic 

matter. 

Wider regions of the shelf, where circulation patterns retain water for longer periods of time, tend to 

have more persistent and severe oxygen depletion (Figure 4). In September 2007, 8,600 km2

 of the shelf 

had hypoxic bottom waters, covering 63% of the shelf area surveyed (Figure 4), making the OregonWashington shelf the second largest hypoxic region in the continental United States, second only to the 

Gulf of Mexico (which averages roughly 14,000 km2). 

Severe hypoxia events were observed in 2002 (Grantham et al. 2004) and 2006 (Chan et al. 2008). 

From these events, it is clear that in some areas, such as Heceta Bank (just south of Newport), oxygen 

concentrations fall to very low values and can persist through much of the summer, ultimately killing or 

displacing nearly all of the bottom-dwelling organisms. Recent work on the impacts of hypoxic waters 

on the development of copepods indicate that oxygen concentrations below 1 ml/L (or 1.43 mg/L) greatly 

reduces the hatching rate of copepod eggs (Peterson unpublished). In instances where copepods are 

not able to move out of hypoxic zones, the reduced hatching rate may also be accompanied by reduced 

Sept 1998 Sept 1999 Sept 2000 Sept 2001

Sept 2002 Sept 2003 Sept 2004 Sept 2005

Sept 2006

Depth (m)

Longitude (W)

Sept 2007 Sept 2008

Figure 3. Oxygen concentration along a 46 km (25 mile) transect across the Oregon shelf (NH Line off Newport, Oregon). 

The thick, red contour indicates the region of hypoxia (1.4 ml/L). The gray shaded area is the bottom bathymetry. Source: 

Jay Peterson, NOAA/OSU CIMRS.
110 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

egg production (Marcus 2001, Sedlacek and Marcus 2005), severely impacting recruitment of species 

critical to the food web of many commercially important fish species. 

The cause of the hypoxia is driven primarily by an interaction between circulation and biological 

activity. The typical upwelling season extends from April to October. During this time, periods of strong 

winds from the north bring nutrient-rich, low-oxygen waters onto the shelf. The nutrient-rich waters 

are mixed into the surface layer and fuel a highly productive planktonic food chain. However, vertical 

transport of fecal pellets of grazers and sinking of nutrient-depleted phytoplankton blooms results in the 

degradation of massive amounts of organic matter on the sea floor. Depending on the vertical flux and on 

the retention time of the water mass, the oxygen consumption can rapidly lead to hypoxic and even anoxic 

conditions.

Science and Management Actions (to date and planned)

To date, no specific scientific programs have been established to monitor the status of hypoxic zones 

along the Oregon-Washington shelf. The development of hypoxic regions along the coast is primarily 

driven by naturally occurring physical and biological processes. Changes in the amount of nutrients 

upwelled to surface waters, water temperatures, and retention of water masses on the shelf likely 

contribute to the persistence, size, and severity of hypoxic zones. The low oxygen zones have been 

shown to greatly impact bottom-dwelling fishes, shellfish, and other organisms inhabiting the shallow 

banks (i.e., Heceta Bank).

Future Outlook

A coordinated research and monitoring effort aimed at informing resource managers is needed. The 

combination of increased awareness of the spatial extent of hypoxia, its impact on the shelf ecosystem, 

Figure 4. Distribution and extent of hypoxic waters (bold 1.4 ml/L contour) along the Oregon-Washington shelf. Shown is 

the minimum oxygen value regardless of the depth it occurred (but the minimum values was almost always at the deepest 

sampling). Panels show the extent in September 2006 (far left), and the seasonal progression during 2007 (May, June and 

Sept). The dashed line along the coast represents the 200 m isobath. Data Source: Cheryl Morgan (OSU and CIMRS) 

and Bill Peterson (NOAA NWFSC), project supported by Bonneville Power Administration.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 111

Executive Summary Appendices

and the availability of instruments that can easily be integrated into current scientific programs will 

provide additional data on the timing and extent of hypoxia along the Oregon-Washington shelf. This 

improved understanding may also lead to an ability to forecast the extent and severity of low dissolved 

oxygen along the shelf which could be a useful tool for fishery managers.

Research programs—such as those carried out through the Pacific Coastal Ocean Observing System 

(NOAA), the Partnership for Interdisciplinary Studies of Coastal Oceans (Oregon State University, et 

al.), the Oregon Coastal Ocean Observing System (Oregon State University), the Olympic Coast National 

Marine Sanctuary (NOAA/National Marine Sanctuaries), and the Bonneville Power Administration 

(Oregon State University, NOAA)—collect hydrographic data, including dissolved oxygen, physical, 

and biological data along the Oregon-Washington shelf. Combined with regional and broad-scale 

hydrographic data, it will be possible to gain a better understanding of the potential mechanisms driving 

the variability of the hypoxic zone. Understanding how natural versus anthropogenically induced changes 

in climate influence the spatial extent and severity of hypoxic zones along the shelf requires consistent, 

long-term observations across the entire region of interest. 

References

Chan F, Barth JA, Lubchenco J, Kirincich A, Weeks H, Peterson WT, Menge BA. 2008. Emergence of Anoxia in the 

California Current Large Marine Ecosystem. Science 319:920

Grantham BA, Chan F, Nielsen KJ, Fox DS, Barth JA, Huyer A, Lubchenco J, Menge BA. 2004. Upwelling-driven 

nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific. Nature 429:749-754

Hickey BM, Banas NS. 2003. Oceanography of the U.S. Pacific Northwest coastal ocean and estuaries with 

application to coastal ecology. Estuaries 26:1010-1031

Marcus NH. 2001. Zooplankton: Responses to the consequences of hypoxia. In: Rabalais NN, Turner RE (eds) 

Coastal and Estuarine Studies: Coastal Hypoxia, Vol 58. American Geophysical Union, Washington D.C., p 49-60

Peterson WT. Unpublished data. National Oceanic and Atmospheric Administration, Northwest Fisheries Science 

Center.

Sedlacek C, Marcus NH. 2005. Egg production of the copepod Acartia tonsa: The influence of hypoxia and food 

concentration. J Exp Mar Biol Ecol 318:183-190.
112 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Yaquina Bay

Physical Description of the System

Yaquina Estuary is a small, drowned, river 

valley estuary located along the central Oregon 

coast of the United States (Figure 1) with an 

estuarine surface area of 19 square kilometers 

(km2) and a watershed area of 650 km2 (Lee et 

al. 2006). Approximately 48% of the estuarine 

area is intertidal. November through April 

(wet season) is a period of high precipitation 

along the Oregon coast when the estuary is 

river dominated. From May through October 

(dry season) the estuary switches from riverine 

to marine dominance and a saltwedge extends 

fairly far upriver. Two tributaries, the Yaquina 

River and Big Elk Creek, with similarly sized 

drainage areas, contribute approximately 

equally to the long-term median freshwater 

inflow of 7.5 cubic meters per second (m3

/s). 

The estuary is well mixed under low flow 

conditions, and partially- to well-mixed during winter high inflow conditions. Tides are semidiurnal with 

a mean tidal range of approximately 1.9 m (Shirzad et al. 1989). The estuary is divided into two zones, 

one of which is dominated by ocean input (Zone 1) and the other which is more influenced by watershed 

and point source inputs (Zone 2). 

Due to the small volume of the estuary and the strong tidal forcing, there is close coupling between the 

estuary and the coastal ocean. Approximately 70% of the volume of the estuary is exchanged with the 

coastal ocean during each tidal cycle (from Brown et al. 2007, Bricker et al. 1998). Like other estuaries in 

the Pacific Northwest that are adjacent to the California Current System, Yaquina Estuary is influenced by 

seasonal wind-driven upwelling which moves relatively cool, nutrient-rich water into the estuary during 

April through September. 

History of Hypoxia (issue, causes, economic and 

ecosystem impacts)

The Yaquina watershed is heavily forested with deciduous, evergreen, and shrub land-use classes 

constituting 85% of the watershed (Lee et al. 2006, based on NOAA 2001 Coastal Change Analysis 

Program data). Although primarily forested and showing little “urban footprint,” the watershed has been 

impacted by a variety of disturbances, including logging which began in the mid-1800s and continues 

to the present. In addition to the direct effects of logging on erosion and water quality, rafting of logs 

can also affect aquatic habitats by physical disturbance, alteration of flow regimes, and accumulation of 

wood and bark debris and sawdust which can smother the benthos and result in low dissolved oxygen 

and/or elevated hydrogen sulfide (Sedell et al. 1991). There are three other nutrient sources influencing 

low dissolved oxygen in the Yaquina Estuary: sewage from municipal discharges, industrial discharges, 

and nonpoint sewage inputs specifically from septic systems. The Yaquina Estuary watershed contains 

Figure 1. Location map of Yaquina Estuary in Oregon. The estuary 

is divided into “marine dominated” (Zone 1) and “riverine dominated” 

(Zone 2) segments (Lee et al. 2006) based on the relative proportion 

of oceanic-derived nutrients versus terrestrially derived nutrients (from 

Brown et al. 2007).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 113

Executive Summary Appendices

the cities of Toledo and Newport; however, only the “Bay Front” of Newport lies within the watershed 

boundaries.

Although the National Estuarine Eutrophication Assessment (Bricker et al. 2007) reported that 

Yaquina has only low level problems with dissolved oxygen, there are strong seasonal patterns within 

the estuary (Figure 2). Oxygen levels in the estuary are comparatively stable during the wet season, but 

show a decline during the dry season. The wet season dissolved oxygen values have an overall mean of 

9.7 mg/L, which is well above the threshold considered to be hypoxic, indicating no significant problems. 

The dry season data show a decline to an overall mean value of 5.8 mg/L but it increases again to wet 

season values. Zone 1 (marine-dominated) and Zone 2 (riverine-dominated) follow the same pattern, but 

Zone 2 appears to have the lower values overall. The lowest values during the dry season are approaching 

hypoxic conditions (< 2 mg/L). However, even during the dry season, most values are above the 

threshold considered to be hypoxic, indicating minimal problems with dissolved oxygen in this system. 

During 1960–1984, there was a noted improvement in dissolved oxygen concentrations in Zone 2 

(riverine-dominated), but it is not clear if the cause of the observed trend was from the decrease in logging 

or the improved sewage treatment. Recent (2002-2006) dissolved oxygen levels in Zone 2 are similar 

to dissolved oxygen levels during the mid-1980s, suggesting that there have been no recent changes in 

dissolved oxygen levels. 

Since 2002, there has been an increase in the incidence of hypoxic events on the Oregon shelf 

(Grantham et al. 2004) that have the potential to influence dissolved oxygen levels within the estuary, 

especially during periods of low oxygen water upwelling (and particularly in Zone 1). Data collected 3.7 

km from the mouth of the estuary show that hypoxic shelf water is imported into Yaquina Estuary during 

Figure 2. Seasonal pattern (1960-1984) of dissolved oxygen at all locations in the Yaquina Estuary and River with squares 

and triangles representing samples from Zones 1 (oceanic dominated) and 2 (river dominated), respectively. Solid line is 

nonlinear least-squares fit to data, which was modeled as a constant during wet season and a cosine function of date during 

the dry season (n = 869; from Brown et al. 2007).
114 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

flood tides. A time series of dissolved 

oxygen and salinity data measured 

during July 9-19, 2002, coinciding with 

a documented hypoxic event on the 

Oregon shelf off of Newport, Oregon 

(Grantham et al. 2004), shows the 

import of hypoxic shelf water into the 

estuary (Figure 3a). Minimum dissolved 

oxygen levels occurred during maximum 

salinities, coincident with flooding tides. 

In addition, minimum dissolved oxygen 

levels occur during minimum water 

temperatures (~ 9 degrees C), which is 

indicative of recently upwelled water. 

These results show that, like other 

Pacific Coast estuaries, dissolved oxygen 

conditions in the lower portion of the 

estuary are strongly influenced by ocean 

conditions due to close coupling between 

the shelf and the estuary resulting from 

strong tidal forcing and upwelling during 

the wet season. Although this has been 

reported with increasing frequency recently, it is not a new phenomenon. A study of the Yaquina Estuary 

attributed low dissolved oxygen concentrations (5 mg/L) in the lower estuary to coastal upwelling during 

July 1968 (Gibson 1974).

Science and Management Actions (to date and planned) 

In response to observed problems with sewage in the early 1900s, a combined stormwater/sewage 

system that discharged raw sewage into the Yaquina River was constructed in Toledo in 1926, and then 

upgraded in 1954 to a primary treatment facility to handle the municipal waste from the city of Toledo. 

This facility, which discharges into the Yaquina Estuary (about 22 km from the mouth of the estuary), 

was upgraded to secondary treatment in 1981. In the late 1980s and early 1990s, the city of Toledo made 

improvements to their stormwater collection system, reducing the bypassing of the treatment plant during 

high flow periods. In 1996, the Toledo plant had a discharge of 0.979 million gallons per day with a 

design capacity of 3.5 million gallons per day (www.epa.gov/OW-OWM.html/mtb/cwns/1996report2/

or.htm).

In addition to the Toledo municipal discharge, a number of houses along the Yaquina Estuary and River 

have on-site septic systems, some which were previously failing. The primary environmental impact of 

these septic systems appears to be microbial contamination and they have all been repaired. A combined 

sewage discharge with a pump station was constructed for Newport in the mid-1950s, which eliminated 

the direct discharge of sewage from Newport into Yaquina Estuary (Brown et al. 2007). A municipal 

sewage system with primary treatment and an offshore discharge was constructed in Newport in 1964, 

which has since been upgraded to secondary treatment.

Addressing issues associated with ocean input of nutrients and the seasonal shift in dominance of 

riverine and oceanic loading is critical in the process of developing nutrient criteria for estuaries in 

the Pacific Northwest region. Several studies have been conducted to try to understand sources and 

variability in order to develop appropriate nutrient criteria and management measures.

Figure 3. a) Time-series of dissolved oxygen and salinity and b) salinity 

versus dissolved oxygen showing import of hypoxic ocean water at a station 

3.7 km from mouth of estuary (from Brown et al. 2007).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 115

Executive Summary Appendices

Future Outlook

Although presently hypoxia is not a significant problem in this estuary, it may worsen in the future 

since the population of Lincoln County, where Toledo and Newport are located, is predicted to increase 

by 12% by 2020. It is possible that conditions will remain the same, if wastewater treatment and other 

land-based nutrient management measures are maintained and improved. However, hypoxia and 

other nutrient-related problems may worsen due to the additional nutrient loads associated with the 

population increase if nutrient management infrastructures are overloaded. This is particularly true in 

Zone 2 (riverine-dominated), since this zone is more influenced by land-based sources of nutrients than 

Zone 1. Historical reduction of dissolved oxygen in Zone 2 suggests that this system can be impacted 

by watershed activities even in the presence of strong flushing. However, if the population of Newport 

increases, water quality in the lower estuary may also worsen as a result. The import of low dissolved 

oxygen water into the estuary from the coastal ocean may result in this system being susceptible to 

hypoxia in the future.

References

Bricker S, Longstaff B, Dennison W, Jones A, Boicourt K, Wicks C, Woerner J. 2007. Effects of Nutrient Enrichment 

in the Nation’s Estuaries: A Decade of Change, National Estuarine Eutrophication Assessment Update. NOAA 

Coastal Ocean Program Decision Analysis Series No. 26. National Centers for Coastal Ocean Science, Silver 

Spring, MD. 322 pp. http://ccma.nos.noaa.gov/news/feature/Eutroupdate.html 

Bricker S, Clement C, Frew S, Harris M, Pirhalla D. 1998. NOAA’s Estuarine Eutrophication Survey. Volume 5: 

Pacific Coast Region. Silver Spring, MD. Office of Ocean Resources Conservation Assessment. 75 pp.

Brown CA, Nelson WG, Boese BL, DeWitt TH, Eldridge PM, Kaldy JE, Lee II H, Power JH, Young DR. 2007. An 

Approach to Developing Nutrient Criteria for Pacific Northwest Estuaries: A Case Study of Yaquina Estuary, 

Oregon. USEPA Office of Research and Development, National Health and Environmental Effects Laboratory, 

Western Ecology Division. EPA/600/R-07/046.

Gibson GC. 1974. Oyster mortality study- summary report 1966-1972. Fish Commission of Oregon, Management and 

Research Division. United States Department of Commerce, National Marine Fisheries Service. 37 pp.

Grantham BA, Chan F, Nielsen KJ, Fox DS, Barth JA, Huyer A, Lubchenco J, Menge BA. 2004. Upwelling-driven 

nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific. Nature 429:749-754.

Lee H. II, Brown CA, Boese BL, Young DR (eds.). 2006. Proposed Classification Scheme for Coastal Receiving 

Waters Based on SAV and Food Web Sensitivity to Nutrients, Volume 2: Nutrient Drivers, Seagrass Distributions, 

and Regional Classifications of Pacific Northwest Estuaries, United States Environmental Protection Agency 

Report, Office of Research and Development, National Health and Environmental Effects Laboratory. Internal 

Report.

Sedell JR, Leone N, Duval WS. 1991. Water Transportation and Storage of Logs. In: Influences of Forest and 

Rangeland Management on Salmonid Fishes and Their Habitats. American Fisheries Society Special Publication 

19:325-368.

Shirzad FF, Orlando SP, Klein CJ, Holliday SE, Warren MA, Monaco ME. 1989. National estuarine inventory: 

Supplement 1, Physical and Hydrologic characteristics, The Oregon estuaries., National Oceanic and Atmospheric 

Administration, Rockville, MD. 
116 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendices

Hood Canal

Physical Description of the System

Despite its name, Hood Canal is a natural formation which 

has experienced hypoxia periodically dating back centuries 

(Brandenberger et al. 2009). It is a sub-basin of Puget Sound, 

Washington, with a fjord-like structure (Figure 1), including a 

natural sill at the mouth which restricts circulation with greater 

Puget Sound; it has a surface area of 386 square kilometers (km2) 

(King County 2001). Restricted and slow circulation coupled 

with a strong salinity stratification and high productivity make it 

conducive to low dissolved oxygen conditions (Newton 2007). 

History of Hypoxia (issue, causes, 

economic and ecosystem impacts)

Hypoxic events have increased in intensity, duration, and 

spatial extent since the 1990s, causing fish kills that prompted the 

Washington State Department of Fish and Wildlife to close many 

fisheries in Hood Canal in 2003. Southern Hood Canal, towards Lynch Cove (Figure 2), has experienced 

more hypoxia than the rest of the canal, and the measured dissolved oxygen concentrations are now lower 

in this area than they were in the 1950s and 1960s (Newton 2007). Hypoxia also develops seasonally 

along the main stem of Hood Canal, and transient upwelling of these waters caused by wind events has 

caused fish kills that garnered considerable public attention. Mortality events of living resources have 

been reported back to the 1920s (Fagergren et al. 2004). Ecosystem impacts such as these, however, 

have increased in frequency since 2002 including an extensive event in September 2006 (Newton 2007). 

Nitrogen inputs, especially from the Lynch Cove area, 

have been implicated, but nitrate from inflowing seawater 

(Paulson et al. 2006), changes in circulation and flushing 

(e.g., modified river flows), stratification, and algal blooms 

are also important (HCDOP 2007).

Science and Management Actions 

(to date and planned) 

As a result of heightened attention to Hood Canal 

environmental deterioration, two significant developments 

may lead to improvements in hypoxia in the future. First, 

the Hood Canal Dissolved Oxygen Program (http://www.

hoodcanal.washington.edu/index.jsp), a partnership of 28 

organizations, including NOAA, EPA, USGS, USACE, 

and the U.S. Navy, was created in 2005 to study oxygen 

dynamics through broad-scale community involvement, 

concerted assessments, and development of models. In 

addition to the Hood Canal Dissolved Oxygen Program, 

but operating on a larger scale, the Puget Sound Partnership 

(http://www.psp.wa.gov/), a new state agency, was 

Figure 1. Diagram of Cross Section of Hood 

Canal with prevailing geography and physical 

conditions (Newton 2007).

Figure 2. August 2006 interpolation reflecting typical 

pattern of low DO concentrations in Hood Canal 

(Newton 2007).
Scientific Assessment of Hypoxia in U.S. Coastal Waters 117

Executive Summary Appendices

established in 2007 to develop a coordinated, region-wide response to the deterioration of the Sound. The group 

adopted an ambitious action plan in 2008. 

Future Outlook

The factors driving hypoxia in Hood Canal are still being clarified, especially the role of nutrients derived from 

human activities. Creation of the Puget Sound Partnership in 2007—which represents a broad coalition of citizen, 

Federal, state, and tribal agencies and interests—should allow development of deliberate protection actions for 

Puget Sound, and Hood Canal specifically. It is important to develop a comprehensive management plan before 

the situation worsens given the expected growth in the coastal population around Puget Sound. 

References

Brandenberger JM, Louchouarn P, Crecelius EA. 2009, submitted. Historical reconstruction of redox sensitive metals in two 

basins of Puget Sound: Evaluating Natural and Post Urbanization Signatures of Hypoxia. Submitting to Geochimica et 

Cosmochimica Acta.

Fagergren D, Criss A, Christensen D. 2004. Hood Canal low dissolved oxygen: Preliminary assessment and corrective action 

plan: Olympia, Washington, Puget Sound Action Team, Publication #PSAT04-06, 43 pp. plus appendices.

HCDOP (Hood Canal Dissolved Oxygen Program). 2007. http://www.hoodcanal.washington.edu/observations/

historicalcomparison.jsp

King County. 2001. Features Of Puget Sound Region: Oceanography And Physical Processes, Chapter 3 of the State of the 

Nearshore Report, King County Department of Natural Resources, Seattle, WA, 2001.

Newton JA. 2007. Hood Canal, WA: The complex factors causing low dissolved oxygen events require ongoing research, 

monitoring, and modeling. In: Bricker S, Longstaff B, Dennison W, Jones A, Boicourt K, Wicks C, Woerner J. 2007. Effects 

of Nutrient Enrichment in the Nation’s Estuaries: A Decade of Change, National Estuarine Eutrophication Assessment 

Update. NOAA Coastal Ocean Program Decision Analysis Series No. 26. National Centers for Coastal Ocean Science, 

Silver Spring, MD. 322 pp. http://ccma.nos.noaa.gov/news/feature/Eutroupdate.html 

Paulson AJ, Konrad CP, Frans LM, Noble M, Kendall C, Josberger EG, Huffman RL, Olsen TD. 2006. Freshwater and saline 

loads of dissolved inorganic nitrogen to Hood Canal and Lynch Cove, western Washington: U.S. Geological Survey 

Scientific Investigations Report 2006-5106, 92 pp.
118 Scientific Assessment of Hypoxia in U.S. Coastal Waters

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Great Lakes Region

Michigan Lake Huron, 

Central Basin

None 1990 Ahrnsbrak and Wing 

1998

Michigan Lake Michigan, 

Central Basin

None 1990 Ahrnsbrak and Wing 

1998

Michigan Lake Superior, 

Central Basin

None 1990 Ahrnsbrak and Wing 

1998

New York Lake Ontario, 

Kingston Basin

Documented 1990 Ahrnsbrak and Wing 

1998

New York Lake Ontario, 

Main Basin

None 1990 Ahrnsbrak and Wing 

1998

New York Lake Ontario, 

Prince Edward 

Bay

Concern 1990 Ahrnsbrak and Wing 

1998

Ohio Lake Erie, 

Central Basin

Documented 1700 Suitable whitefish 

habitat reduced 

by low dissolved 

oxygen. Benthos 

reduced.

Periodic hypolimnetic anoxia 

prior to European settlement. 

Global warming will lower 

dissolved oxygen from higher 

microbial metabolism. Increase 

in anoxia from 1930s to 1970s.

Hartman 1972, 

Krieger 1985, Rosa 

and Burns 1987, 

Delorme 1982, 

Edwards et al. 

2005, Blumberg and 

DiToro 1990, Krieger 

et al. 2007

Ohio Lake Erie, 

Eastern Basin

None 1990 Ahrnsbrak and Wing 

1998

Ohio Lake Erie, 

Western Basin

Documented 1950 Mortality of 

mayflies in 1953. 

Mayfly populations 

partially recovered 

in 1990s.

Occasional hypoxia, improved 

in 1990s.

Britt 1955, Krieger 

1985, Gerlofsma and 

Ciborowski 1999

Gulf of Mexico Region

Alabama Alabama Inner 

Shelf

Documented 1990 Area off Dauphin Island 

hypoxic. Dissolved oxygen 

declined from 1980s to 1990s.

Rabalais et al. 1985, 

Rabalais 1998, 

Byrnes et al. 1999

Alabama Bon Secour Bay Documented 2000 Mortality of benthos 

and loss of oysters.

Rikard et al. 2000

Appendix III. Table of U.S. Systems 

Impacted by Hypoxia

Table A1. Systems in the United States by region and their dissolved oxygen condition. 

Regions are based on Bricker et al. 2007. Analysis current through December 2008.

Documented indicates systems with low dissolved oxygen measurements leading to hypoxia and 

evidence that hypoxia was caused, at least in part, by human activity—mainly related to eutrophication, but also hydraulic modifications such as dams and canal construction.

Concern indicates systems that exhibit primary or secondary effects of eutrophication, including 

elevated nutrient levels, elevated chlorophyll levels, or harmful algal blooms. These systems are 

impaired by nutrients and are possibly at risk of developing hypoxia. Some of the systems classified 

as areas of concern may already be experiencing hypoxia, but there is a lack dissolved oxygen data. 

None indicates systems with no measured low dissolved oxygen and with low expression of primary 

or secondary effects of eutrophication.
Scientific Assessment of Hypoxia in U.S. Coastal Waters 119

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Alabama Meaher Park Documented 2000 Data is from water quality 

monitoring stations.

Mobile Bay NEP 

2008

Alabama Mobile Bay Documented 1860 Occasional 

shoreward migration 

of hypoxia stressed 

fish and crustaceans 

(Jubilees).

May have been hypoxic in 

1800s. Has winter hypoxia. 

Stratification a major factor. 

Some improvement in 

dissolved oxygen between 

1900s and 2000s.

Pennock et al. 1994, 

May, 1973, Loesch 

1960, Engle and 

Summers 1999, 

Rabalais et al. 1985, 

Bricker et al. 1999, 

2007

Alabama Mobile River Concern 1980 Rabalais et al. 1985

Alabama Tensaw River Concern 1980 Rabalais et al. 1985

Alabama Weeks Bay Documented 1990 Mangrove area. Sanger et al. 2002

Alabama Wolf Bay Documented 1980 Part of regional water quality 

monitoring program.

Engle et al. 1999, 

Rabalais et al. 1985

Florida Alafia River Documented 1980 Windsor 1985

Florida Alaqua Creek None 1980 Windsor 1985

Florida Allen Creek Concern 1980 Windsor 1985

Florida Alligator Alley 

Canal

Documented 1970 Windsor 1985

Florida Alligator Creek Concern 1980 Windsor 1985

Florida Apalachee Bay Documented 1970 Localized hypoxia and 

anoxia in 1970s attributed 

to pulp mills in Econfina 

and Fenholloway Rivers, 

some dissolved oxygen 

improvements from1990s to 

2000s.

Windsor 1985, 

Bricker et al. 

1999, Heck 1976, 

Livingston 1975

Florida Apalachicola 

Bay

Documented 1990 No hypoxia in 1980s, observed 

in 1990s. Some improvement 

in dissolved oxygen in 2000s.

Lowery 1998, Sanger 

et al. 2002, Windsor 

1985, Bricker et al. 

1999

Florida Apalachicola 

River

None 1980 Windsor 1985

Florida Aucilla River Concern 1980 Windsor 1985

Florida Bayou Chico Documented 1990 Summers et al. 1997

Florida Bayou Marcus 

Creek

Documented 1980 Windsor 1985

Florida Bear Creek Concern 1980 Windsor 1985

Florida Big Lagoon Documented 1990 Not hypoxic in 1980s. Part 

of regional water quality 

monitoring program.

Whitledge 1985, 

Engle et al. 1999

Florida Big Lostman's 

Bay

Concern 1980 Windsor 1985

Florida Blackwater River None 1980 Windsor 1985

Florida Caloosahatchee 

River

Documented 1990 Windsor 1985, 

Bricker et al. 1997, 

2007

Florida Carpenters 

Creek/Bayou 

Texar

Concern 1980 Windsor 1985

Florida Carrabelle River None 1980 Windsor 1985
120 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Florida Charlotte Harbor Documented 1980 1980s to 1990s 

improvement 

in water quality 

from nutrient 

management, 2000s 

decline in water 

quality as population 

expanded.

Dissolved oxygen declined 

from 1970s to 1990s, than 

increased to 1970s levels by 

end of 1990s, declined again in 

2000s. Associated wet season 

and stratification, hurricane 

disturbance resulted in more 

low dissolved oxygen.

Tomasko et al 2006, 

Turner et al. 2006, 

Windsor 1985

Florida Chatham Bay/

River

Concern 1980 Windsor 1985

Florida Choctawhatchee 

Bay

Documented 1980 Some improvement in 

dissolved oxygen between 

1990s and 2000s.

Lowery 1998, 

Windsor 1985, 

Bricker et al. 1999, 

2007

Florida Choctawhatchee 

River

None 1980 Windsor 1985

Florida Clowers Creek Documented 1980 Windsor 1985

Florida Cross Bayou 

Canal

Documented 1980 Windsor 1985

Florida Crystal Bay Concern 1980 Windsor 1985

Florida Crystal River Concern 1980 Windsor 1985

Florida Deadman Bay None 1980 Windsor 1985

Florida Deerpoint Lake Concern 1980 Windsor 1985

Florida Delaney Creek Documented 1990 Windsor 1985

Florida East Bay, 

Pensacola

Documented 1980 Some improvement in 

dissolved oxygen between 

1980s and 2000s. Improved 

from nutrient management, 

municipal and industrial.

Windsor 1985

Florida East Bay, 

Apalachicola

None 1980 Windsor 1985

Florida Econfina Creek None 1980 Windsor 1985

Florida Econfina River Documented 1970 Some hypoxia in 1970s, 

dissolved oxygen improved 

with effluent control. Winter 

and summer hypoxia.

Windsor 1985, 

Livingston 1975

Florida Eleven Mile 

Creek

Documented 1980 Windsor 1985

Florida Escambia Bay Documented 1960 Loss of fisheries 

species, fish kills.

Summers et al. 1997, 

Windsor 1985

Florida Escambia River None 1980 Windsor 1985

Florida Everglades GAC 

Canal

Documented 1970 Windsor 1985

Florida Fenholloway 

River

Documented 1970 Hypoxia and anoxia in 

1970 attributed to pulp mill 

effluents. Dissolved oxygen 

improved with effluent control. 

Winter and summer hypoxia 

and anoxia.

Windsor 1985, 

Livingston 1975
Scientific Assessment of Hypoxia in U.S. Coastal Waters 121

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Florida Florida Bay Documented 2000 Some improvement in 

dissolved oxygen between 

1990s and 2000s but hypoxic 

events may be more frequent 

in 2000s.

Bricker et al. 1999, 

2007, TIEE 2008

Florida Gordon River Documented 1980 Windsor 1985

Florida Hillsborough 

Bay

Documented 1970 Almost complete 

mortality of benthos 

in late summer.

Improved from nutrient 

management.

Santos and Simon 

1980, Windsor 1985, 

Bricker et al. 2007

Florida Hillsborough 

River

Documented 1980 Windsor 1985

Florida Inner Continental 

Shelf

Documented 2000 Mortality of 

benthos. Mortality 

of fishes from 

combined effects 

of HAB and low 

dissolved oxygen.

Low dissolved oxygen from 

HAB (toxic dinoflagellate 

Karenia brevis) in August 

2005. Multiple stressors 

involved in mortalities.

Landsberg 2009

Florida Jones and 

Jackson Creeks

Documented 1980 Windsor 1985

Florida Lake 

Panasoffkee

None 1980 Windsor 1985

Florida Lake Rousseau None 1980 Windsor 1985

Florida Little Aucilla 

River

Documented 1980 Windsor 1985

Florida Long Bayou Documented 1980 Windsor 1985

Florida Looe Key Documented 1980 Mortality of benthos 

and corals.

General eutrophication 

affecting water quality, 

dissolved oxygen conditions 

worsened from 1990s to 2000s. 

Rainfall events followed 

by low dissolved oxygen in 

seagrass and coral reef areas.

Lapointe and Matzie 

1996, Whitledge 

1985, Bricker et al. 

2007

Florida Martin Bayou Concern 1980 Windsor 1985

Florida Mulatto and 

Indian Bayous

Documented 1980 Windsor 1985

Florida Munson Slough Documented 1980 Windsor 1985

Florida Myakka River Documented 1980 Combination of agricultural 

runoff and swamp drainage.

Windsor 1985

Florida North Bay Concern 1980 Windsor 1985

Florida Ochlockonee 

Bay

None 1980 Windsor 1985

Florida Ochlockonee 

River

None 1980 Windsor 1985

Florida Old River Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Florida Otter Creek None 1980 Windsor 1985

Florida Patch Reef Documented 1990 Mortality of 

benthos.

Rainfall events followed 

by low dissolved oxygen in 

seagrass and coral reef areas.

Lapointe and Matzie 

1996

Florida Peace River Documented 1980 Hurricanes 

worsened hypoxia in 

2004.

Worse after hurricanes in 2004. 

Algal blooms from nutrients 

and sewage.

Windsor 1985, 

Tomasko et al. 2006, 

Turner et al. 2006
122 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Florida Pensacola Bay Documented 1960 Loss of fisheries 

species, fish kills. 

Reduction in shrimp 

catch starting in 

1960s attributed to 

multiple stressors 

including low 

dissolved oxygen.

Some improvement in 

dissolved oxygen between 

1980s and 2000s.

Lowery 1998, Hagy 

et al. 2006, Windsor 

1985, Hagy and 

Murrell 2007

Florida Perdido Bay Documented 1960 Dissolved oxygen poor in 

1960s, but improved 1970s 

to 1980s. Dissolved oxygen 

declined from 1990s to 2000s. 

Stratification and industrial 

effluents highly significant 

factors, high nutrient loads.

Flemer et al. 1999, 

Whitledge 1985, 

Bricker et al. 1999, 

2007

Florida Perdido River Documented 1960 Windsor 1985

Florida Philippi Creek Documented 1980 Windsor 1985

Florida Pine Channel Documented 1990 Mortality of 

benthos.

Rainfall events followed 

by low dissolved oxygen in 

seagrass and coral reef areas.

Lapointe and Matzie 

1996

Florida Port Pine Documented 1990 Mortality of 

benthos.

Rainfall events followed 

by low dissolved oxygen in 

seagrass and coral reef areas.

Lapointe and Matzie 

1996

Florida Rocky Creek None 1980 Windsor 1985

Florida Rookery Bay Documented 1990 Dissolved oxygen levels 

declined from 1990s to 2000s.

Rabalais 1998, 

Sanger et al. 2002, 

Bricker et al. 1999, 

2007

Florida Santa Rosa 

Sound

None 1980 Windsor 1985

Florida Sarasota Bay Documented 1980 SAV recovering. Dissolved oxygen levels 

improved from 1990s to 2000s.

Windsor 1985, 

Bricker et al. 1999, 

2007

Florida Sopchoppy River None 1980 Windsor 1985

Florida Spring Warrior 

Creek

None 1980 Windsor 1985

Florida St. Andrew Bay Documented 1970 Hypoxia reduced from nutrient 

management, municipal and 

industrial.

Windsor 1985

Florida St. George 

Sound

Documented 1990 No dissolved 

oxygen problem in 

1980s.

Part of regional water quality 

monitoring program.

Engle et al. 1999, 

Windsor 1985

Florida St. Joseph Bay Documented 1990 Avoidance by 

mobile fauna and 

brittlestar migration.

Was not hypoxic in 1980s. Windsor 1985, 

Leonard and 

McClintock 1999

Florida St. Marks River None 1980 Windsor 1985

Florida Steinhatchee 

River

None 1980 Windsor 1985

Florida Suwannee River Concern 1980 Windsor 1985
Scientific Assessment of Hypoxia in U.S. Coastal Waters 123

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Florida Tampa Bay Documented 1980 SAV recovering. Improved conditions for 

dissolved oxygen from 1980s 

to 1990s, dissolved oxygen 

worsened from 1990s to 

2000s. Improved from nutrient 

management.

Leverone 1995, 

Lowery 1998, 

Bricker et al. 1999, 

2007

Florida Ten Mile Creek None 1980 Windsor 1985

Florida Ten Thousand 

Islands North

Documented 2000 Bricker et al. 1999, 

2007

Florida Ten Thousand 

Islands South

Documented 2000 Bricker et al. 1999, 

2007

Florida Turkey Creek None 1980 Windsor 1985

Florida Useppa Island Documented 1940 Some fish mortality. Low dissolved oxygen from 

HAB (Gymnodinium).

Gunter et al. 1948

Florida Waccasassa Bay None 1980 Windsor 1985

Florida Wakulla River Concern 1980 Windsor 1985

Florida Watson Bayou Documented 1980 Part of regional water quality 

monitoring program.

Windsor 1985, Engle 

et al. 1999

Florida Weeki Wachee 

Springs

Documented 1980 Windsor 1985

Florida West Bay Concern 1980 Windsor 1985

Florida Whitaker Bayou Documented 1980 Windsor 1985

Florida Withlacoochee 

River

Concern 1980 Windsor 1985

Florida Yellow River None 1980 Windsor 1985

Louisiana Amite River Documented 1990 Reduced benthos 

and loss of large 

clams.

Penland et al. 2002 

(http://pubs.usgs.gov/

of/2002/of02-206/

index.html)

Louisiana Atchafalaya Bay Documented 2000 Not hypoxic in 1980s. 

Stratification highly significant 

factor.

Rabalais et al. 1985, 

Bricker et al. 2007

Louisiana Atchafalaya 

River

None 1980 Rabalais et al. 1985, 

Bricker et al. 2007

Louisiana Balize Delta Documented 1950 Low dissolved oxygen present 

in 1950s based on foraminifera 

proxies.

Brunner et al. 2006

Louisiana Barataria Bay Documented 1950 Not hypoxic in 1980s. Rabalais et al. 1985, 

Bricker et al. 2007, 

Engle et al. 1999

Louisiana Blind Bay Concern 1990 Engle et al. 1999

Louisiana Breton Sound Documented 1990 Not hypoxic in 1980s. Rabalais et al. 1985, 

Bricker et al. 2007, 

Engle et al. 1999

Louisiana Caillou Bay None 1980 Rabalais et al. 1985

Louisiana Calcasieu 

Estuary

Concern 1980 Whitledge 1985

Louisiana Calcasieu Lake Concern 1980 Some improvement in 

dissolved oxygen levels 

between 1990s and 2000s.

Rabalais et al. 1985, 

Bricker et al. 1999, 

2007
124 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Louisiana Calcasieu Pass/

Channel

Concern 1980 Rabalais et al. 1985, 

Bricker et al. 2007

Louisiana Chandeleur 

Sound

Documented 1990 Not hypoxic in 1980s. Rabalais et al. 1985, 

Bricker et al. 2007, 

Engle et al. 1999

Louisiana East Cote 

Blanche Bay

None 1980 Rabalais et al. 1985

Louisiana Graden Island 

Bay

Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Louisiana Grand Bay Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Louisiana Lake Boudreaux None 1980 Rabalais 1998

Louisiana Lake 

Cataouatche

Documented 1970 Fish kills. Rabalais 1998

Louisiana Lake Maurepas None 1970 Rabalais 1998

Louisiana Lake Penchant Concern 1980 Low dissolved 

oxygen may have 

caused bass to leave 

the lake.

Rabalais et al. 1985

Louisiana Lake 

Pontchartrain

Documented 1970 Reduced species 

diversity. Loss of 

large clams.

250 km2

 USGS estimate. Abadie and Poirrier 

2000, Rabalais et al. 

1985, Penland et al. 

2002

Louisiana Lake Tambour None 1980 Rabalais 1998

Louisiana Mermentau 

River

None 1990 Bricker et al. 1997

Louisiana Mississippi/

Atchafalaya 

River Plumes

Documented 1970 Avoidance by 

mobile fauna. 

Mortality of 

benthos with annual 

recolonization, Loss 

of biomass.

Area coincides with historic 

white and brown shrimp 

fishing grounds. Annual 

hypoxia developed in 1970s, 

is now the largest hypoxic 

area in US. Major events in 

Mississippi watershed may 

have led to low dissolved 

oxygen prior to 1700s.

Turner and Rabalais 

1994, Justic et al. 

1996, Sen Gupta et 

al. 1996, Rabalais et 

al. 2007, Rabalais 

and Turner 2001, 

Osterman et al. 2007, 

Craig and Crowder 

2005

Louisiana Moss Bay None 1980 Rabalais 1998

Louisiana Terrebonne Bay Concern 1980 Rabalais et al. 1985

Louisiana Timbalier Bay None 1980 Rabalais et al. 1985

Louisiana Vermilion Bay Documented 2000 Not hypoxic in 1980s. 

Stratification highly significant 

factor.

Rabalais et al. 1985, 

Bricker et al. 2007

Louisiana Wax Lake Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Louisiana West Cote 

Blanche Bay

None 1980 Rabalais et al. 1985

Louisiana West Hackberry Documented 1980 Mortality 

with annual 

recolonization.

Associated with brine seep. Gaston 1985

Mississippi Back Bay Documented 1970 Low dissolved oxygen occurs 

but not a recurring problem in 

1980s. Part of regional water 

quality monitoring program.

Engle et al. 1999, 

Rabalais et al. 1985
Scientific Assessment of Hypoxia in U.S. Coastal Waters 125

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Mississippi Bayou Casotte/

Chico

Documented 1970 Rabalais 1998

Mississippi Bayou La Batre Concern 1980 Rabalais 1998

Mississippi Big Lake Documented 1980 Episodic algal blooms. Rabalais et al. 1985, 

Rabalais 1998

Mississippi Biloxi Bay Concern 1970 Low dissolved oxygen occurs 

but not a recurring problem in 

1980s.

Engle et al. 1999, 

Rabalais et al. 1985

Mississippi Biloxi River Concern 1990 Rabalais 1998

Mississippi Escatawpa River Documented 1970 Rabalais et al. 1985

Mississippi Jourdan River Concern 1990 Rabalais 1998

Mississippi Lake Borgne Concern 1980 Rabalais et al. 1985

Mississippi Little River Concern 1980 Rabalais 1998

Mississippi Mississippi Inner 

Shelf, Deeper

None 1950 Based on foraminifera proxies, 

there was no low dissolved 

oxygen in deeper areas >50 m.

Brunner et al. 2006

Mississippi Mississippi Inner 

Shelf, Shallow

Documented 1950 Sporadic low dissolved oxygen 

in 1800s associated with 

flood events, by 1940s low 

dissolved oxygen increased 

and intensified in 1960s based 

on foraminifera proxies.

Rabalais et al. 1985, 

Brunner et al. 2006

Mississippi Mississippi 

River, Lower

None 1980 Rabalais et al. 1985

Mississippi Mississippi 

Sound East

Documented 1980 Dissolved oxygen improved 

from 1990s to 2000s. 

Stratification highly significant 

factor.

Rabalais et al. 1985, 

Bricker et al. 1999, 

2007

Mississippi Mississippi 

Sound West 

Documented 1950 Low dissolved oxygen in 

1950s, intensified in 1960s 

based on foraminifera proxies.

Rabalais et al. 1985, 

Bricker et al. 2007, 

Brunner et al. 2006

Mississippi Pascagoula Bay Concern 1980 Dissolved oxygen declined 

from 1980s to 1990s.

Rabalais et al. 1985, 

Rabalais 1998

Mississippi Pascagoula River Documented 1970 Hypoxic from March to 

October.

Rabalais 1998

Mississippi Pearl River None 1980 Rabalais et al. 1985, 

Rabalais 1998

Mississippi St. Louis Bay None 1980 Rabalais et al. 1985

Mississippi Tchoutacabouffa 

River

Concern 1990 Rabalais 1998

Mississippi West Fowl River Concern 1980 Rabalais 1998

Mississippi Wolf River None 1990 Rabalais 1998

Texas Alazan Bay Concern 1980 Rabalais 1998
126 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Texas Aransas Bay Documented 2000 Diel hypoxia alters 

nursery value of 

SAV beds. Larval 

red drum, Sciaenops 

ocellatus, growth 

reduced when 

exposed to hypoxia 

>8 hours.

Open Bay had little low 

dissolved oxygen in 1980s. 

Increased nutrient loads lower 

dissolved oxygen in SAV beds.

Lowery 1998, 

Rabalais et al. 1985, 

Perez-Domingues et 

al. 2006

Texas Arroyo Colorado Documented 1980 Hypoxia or anoxia occur yearround.Engle et al. 1999, 

Rabalais et al. 1985

Texas Baffin Bay Documented 1980 Rabalais et al. 1985, 

Bricker et al. 2007

Texas Brazos River Documented 1980 Rabalais et al. 1985, 

Bricker et al. 2007

Texas Brazos Santiago 

Pass

None 1980 Rabalais 1998

Texas Brownsville Ship 

Channel

Documented 1980 Rabalais 1998

Texas Bryan Mound, 

deep

Documented 1980 Decreased diversity 

and abundance of 

mobile species at the 

onset of hypoxia. 

Mortality of 

benthos with annual 

recolonization.

Harper et al. 1981, 

1991

Texas Bryan Mound, 

shallow

Documented 1970 Stressed fishes, mass 

mortality of benthos 

with multi-year 

recovery.

Harper et al. 1981, 

1991

Texas Cayo del Grullo Concern 1980 Rabalais 1998

Texas Cedar Bayou Documented 1980 Rabalais et al. 1985

Texas Chocolate Bay Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Texas Colorado River None 1980 Rabalais et al. 1985

Texas Copano Bay None 1980 Rabalais 1998

Texas Corpus Christi 

Bay

Documented 1980 Reduced, biomass 

at hypoxic stations 

is 96% less than at 

stations with normal 

oxygen levels.

Hypoxia expanded in the 

1990s. Low bottom dissolved 

oxygen when bottom salinity 

was high.

Ritter and Montagna 

1999, Montagna 

and Ritter 2006, 

Montagna and Kalke 

1992, Applebaum et 

al. 2005

Texas Cox Bay None 1980 Rabalais 1998

Texas Dickinson Bayou Documented 1980 Rabalais et al. 1985

Texas East Bay Documented 1980 Whitledge 1985

Texas Espiritu Santo 

Bay

None 1980 Rabalais 1998

Texas Freeport Documented 1970 Avoidance, some 

mortality of fishes. 

Mortality of benthos 

with multi-year 

recovery.

Harper and Rabalais 

1995
Scientific Assessment of Hypoxia in U.S. Coastal Waters 127

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Texas Freeport Ship 

Channel

None 1980 Rabalais et al. 1985

Texas Galveston Bay Concern 1970 Lowery 1998, 

Rabalais et al. 1985

Texas Guadalupe 

Estuary

None 1980 Lowest frequency of low 

dissolved oxygen of all Texas 

estuaries in 1980s.

Rabalais et al. 1985, 

Rabalais 1998

Texas Keller Bay None 1980 Rabalais 1998

Texas Laguna Madre, 

Lower

Documented 1980 Sewage and shrimp farming, 

most low dissolved oxygen 

in deeper areas, diel low 

dissolved oxygen in shallow 

areas.

Ziegler and Benner 

1998, Rabalais et al. 

1985, Bricker et al. 

2007

Texas Laguna Madre, 

Upper

Documented 1980 Stratification highly significant 

factor, most low dissolved 

oxygen in deeper areas.

Rabalais et al. 1985, 

Bricker et al. 2007

Texas Laguna Salada Concern 1980 Rabalais 1998

Texas Lavaca Bay Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Texas Matagorda Bay Documented 1980 Lowery 1998, 

Rabalais et al. 1985, 

Bricker et al. 2007

Texas Matagorda Ship 

Channel

Documented 1980 Rabalais 1998

Texas Mesquite Bay None 1980 Rabalais 1998

Texas Mission Bay None 1980 Rabalais 1998

Texas Mission-Aransas 

Estuary

Documented 1980 Rabalais et al. 1985, 

Rabalais 1998

Texas Nueces Bay Documented 1980 Rabalais 1998

Texas Nueces Estuary Concern 1980 Rabalais 1998

Texas Offatts Bayou Documented 1930 Mass mortality of 

benthos and fishes.

First occurrence 1936. Part 

of regional water quality 

monitoring program.

Gunter 1942, Engle 

et al. 1999, White et 

al. 1984

Texas Oso Bay Concern 1980 Rabalais 1998

Texas Port Arthur 

Canal

Concern 1980 Rabalais et al. 1985

Texas Redfish Bay None 1980 Rabalais 1998

Texas Rio Grand Tidal Concern 1980 Rabalais et al. 1985

Texas Sabine Lake Concern 1980 Rabalais et al. 1985

Texas Sabine Pass Concern 1980 Rabalais et al. 1985

Texas Sabine-Neches 

Estuary

Documented 1980 Rabalais et al. 1985

Texas San Antonio Bay Documented 1980 Dissolved oxygen declined 

from 1980s to 1990s. 

Stratification highly significant 

factor.

Lowery 1998, 

Rabalais et al. 1985

Texas San Antonio 

River

None 1980 Rabalais 1998

Texas San Bernard 

River

Documented 1990 Part of regional water quality 

monitoring program.

Engle et al. 1999

Texas South Bay None 1980 Rabalais 1998
128 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Texas Texas Inner 

Shelf

Concern 1980 Rabalais et al. 1985

Texas Tres Palacios 

Bay

None 1980 Rabalais 1998

Texas Trinity Bay Concern 1980 Whitledge 1985

Texas Trinity-San 

Jacinto Estuary

Concern 1990 Rabalais 1998

Texas Upper Galveston 

Bay Channel

Documented 1980 Part of regional water quality 

monitoring program.

Engle et al. 1999, 

Rabalais et al. 1985

Texas West Bay Concern 1980 Rabalais et al. 1985

Mid-Atlantic Region

Connecticut Ash Creek Documented 1980 Whitledge 1985

Connecticut Black Rock 

Harbor

None 1980 Whitledge 1985

Connecticut Bridgeport 

Harbor

None 1980 Whitledge 1985

Connecticut Burr Creek Documented 1980 Whitledge 1985

Connecticut Connecticut 

River 

Documented 1980 Episodic events in tidal 

freshwater zone.

Whitledge 1985, 

Bricker et al. 2007

Connecticut Housatonic River None 1980 Whitledge 1985

Connecticut Johnson Creek Concern 1980 Whitledge 1985

Connecticut Naugatuck River Concern 1980 Whitledge 1985

Connecticut Pawcatuck River Concern 1980 Whitledge 1985

Connecticut Quinnipiac River Concern 1980 Whitledge 1985

Connecticut Thames River None 1980 Whitledge 1985

Connecticut Yellow Mill 

Channel

Concern 1980 Whitledge 1985

Delaware Bald Eagle 

Creek

Documented 2000 Fish kills. Eutrophication and limited 

tidal exchange with adjacent 

body of water.

Luther et al. 2004

Delaware Blackwater 

Landing

Documented 1990 Sanger et al. 2002

Delaware Dead-end canals/

Inland bays

Documented 1990 Dead-end canals have limited 

tidal exchange with adjacent 

body of water.

Maxted et al. 1997

Delaware Delaware Bay None 1980 Whitledge 1985

Delaware Delaware River Documented 1910 Recovering 

American shad and 

striped bass fishery.

Low dissolved oxygen first 

recorded in 1915. Recovered 

from low dissolved oxygen 

through nutrient management.

Weisberg et al. 1996, 

Summers et al. 1997, 

Patrick 1988

Delaware Indian River Bay Documented 1980 Whitledge 1985

Delaware Little 

Assawoman Bay

Concern 1980 Fish kills. Whitledge 1985, 

Bricker et al. 2007

Delaware Murderkill River Documented 1960 Caused by sewage discharge. deWitt and Daiber 

1974

Delaware Pepper Creek Documented 2000 Fish migrate in 

and out of creek 

depending on 

dissolved oxygen 

levels.

Daily cycle of dissolved 

oxygen from supersaturated to 

hypoxic.

Tyler 2004, Tyler and 

Targett 2007

Delaware Rehoboth Bay Documented 1980 Whitledge 1985

Maryland Anacostia River Concern 1980 Whitledge 1985
Scientific Assessment of Hypoxia in U.S. Coastal Waters 129

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Maryland Assawoman Bay Documented 1980 No hypoxia in 1970s. Whitledge 1985, 

Bricker et al. 2007, 

Boynton et al. 1996

Maryland Back Creek None 1980 Whitledge 1985

Maryland Back River Documented 1980 Whitledge 1985

Maryland Baltimore 

Harbor

Documented 1980 Whitledge 1985

Maryland Big Annemessex 

River

None 1980 Whitledge 1985, 

CBP 2008

Maryland Bird River None 1980 Whitledge 1985

Maryland Bodkin Creek Documented 1980 Whitledge 1985

Maryland Bohemia None 1990 CBP 2008

Maryland Bush River None 1980 Whitledge 1985

Maryland Cabin John 

Creek

Concern 1980 Whitledge 1985

Maryland Chesapeake Bay 

Mainstem

Documented 1930 Low dissolved 

oxygen killed 

crabs in crab 

pots. Mortality of 

benthos with annual 

recolonization.

Seasonal anoxia detected in 

sediment record as far back 

as 1934-1948. Low dissolved 

oxygen events in the 1800s. 

Low dissolved oxygen 

occurrence has increased from 

1980 to 2000, area of hypoxia 

and anoxia has increased.

Zimmerman and 

Canual 2000, 

Newcombe and 

Horne 1938, Officer 

et al. 1984, Seliger 

et al. 1985, Holland 

et al., 1987, Boesch 

et al. 2001, Hagy et 

al. 2004, Kemp et al. 

2005

Maryland Chester River Documented 1980 Avoidance and 

some mortality of 

fishes. Mortality of 

benthos with annual 

recolonization.

Low dissolved oxygen events 

occur in June-Aug. Dissolved 

oxygen declined from 1990s 

to 2000s

Whitledge 1985, 

Bricker et al. 1999, 

2007. CBP 2008

Maryland Chincoteague 

Bay

Concern 1980 No hypoxia in 1970s. Whitledge 1985, 

Bricker et al. 2007, 

Boynton et al. 1996

Maryland Choptank River Documented 1980 Low dissolved oxygen events 

occur in June-Sept.

Whitledge 1985, 

Bricker et al. 2007

Maryland Corsica River Documented 2000 Fish kill from 

combined stress of 

HAB toxins and low 

dissolved oxygen.

Bricker et al. 2007

Maryland Dead-end canals Documented 1990 Dead-end canals have limited 

tidal exchange with adjacent 

body of water.

Maxted et al. 1997

Maryland Eastern Bay None 1990 CBP 2008

Maryland Elk River None 1980 Whitledge 1985

Maryland Fishing Bay None 1990 CBP 2008

Maryland Gunpowder 

River

None 1980 Whitledge 1985, 

CBP 2008
130 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Maryland Honga None 1990 CBP 2008

Maryland Isle of Wight 

Bay

Documented 1980 No hypoxia in 1970s. Whitledge 1985, 

Bricker et al. 2007, 

Boynton et al. 1996

Maryland Jug Bay Documented 1990 Sanger et al. 2002

Maryland Little Choptank None 1990 CBP 2008

Maryland Little River/

Browns Creek

None 1980 Whitledge 1985

Maryland Magothy Documented 1990 CBP 2008

Maryland Manokin None 1990 CBP 2008

Maryland Manokin River Concern 1980 Whitledge 1985

Maryland Mattawoman 

Creek

None 1980 Whitledge 1985, 

CBP 2008

Maryland Middle None 1990 CBP 2008

Maryland Miles River None 1980 Whitledge 1985

Maryland Nanjemoy Creek None 1980 Whitledge 1985

Maryland Nanticoke River None 1980 Whitledge 1985

Maryland Nassawango 

Creek

None 1980 Whitledge 1985

Maryland Newport Bay None 1980 No hypoxia in 1970s. Whitledge 1985, 

Bricker et al. 2007, 

Boynton et al. 1996

Maryland Northeast River None 1980 Whitledge 1985

Maryland Oxon Run Concern 1980 Whitledge 1985

Maryland Patapsco River Documented 1990 Riedel et al. 1999, 

CBP 2008

Maryland Patuxent River Documented 1930 Avoidance, low 

egg hatching/

larval mortality, 

bay anchovy eggs 

killed by hypoxia. 

Mortality of 

benthos with annual 

recolonization.

Duration and spatial extent 

of low dissolved oxygen 

has increased from 1930-79. 

Dissolved oxygen declined 

from 1990s to 2000s. 

Indications that hypoxia 

occurred in 1700s from 

watershed modifications and 

wet periods. Rise in anoxia in 

1970s linked to nutrient runoff 

and wet weather.

Keister et al. 2000, 

Breitburg et al. 1997, 

1997, Bricker et al. 

1999, 2007, Cronin 

and Vann 2003

Maryland Piscataway 

Creek

Concern 1980 Whitledge 1985

Maryland Pocomoke River None 1980 Whitledge 1985

Maryland Port Tobacco 

River

Concern 1980 Whitledge 1985

Maryland Potomac River Documented 1910 Mortality of 

benthos with annual 

recolonization.

Low dissolved oxygen in 

May-Sept; increased spatial 

coverage of hypoxia from 

1910s. Some improvement in 

dissolved oxygen levels from 

1990s to 2000s.

Sale and Skinner 

1917, Whitledge 

1985, Bricker et al. 

1999, 2007, CBP 

2008
Scientific Assessment of Hypoxia in U.S. Coastal Waters 131

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Maryland Rhode River None 1990 CBP 2008

Maryland Rock Creek Concern 1980 Whitledge 1985

Maryland Sassafras River None 1980 Whitledge 1985

Maryland Seneca Creek Concern 1980 Whitledge 1985

Maryland Severn River Documented 1990 CBP 2008

Maryland Sinepuxent Bay Concern 1980 No hypoxia in 1970s. Whitledge 1985, 

Bricker et al. 2007, 

Boynton et al. 1996

Maryland St. Leonard 

Creek

Documented 1990 Summers et al. 1997

Maryland St. Martin River None 1970 No hypoxia in 1970s. Boynton et al. 1996

Maryland St. Marys River Concern 1980 Whitledge 1985

Maryland Susquehanna 

River

Concern 1980 Whitledge 1985

Maryland Swan Creek None 1980 Whitledge 1985

Maryland Tangier Sound Concern 1990 Rabalais 1998, 

Bricker et al. 2007

Maryland Turville Creek None 1970 No hypoxia in 1970s. Boynton et al. 1996

Maryland Wicomico River None 1990 CBP 2008

Maryland Wye River None 1980 Whitledge 1985

Massachusetts Acushnet River Concern 1970 Fish kill, maybe 

dissolved oxygen 

related August 1973.

Whitledge 1985

Massachusetts Apponaganset 

Bay

None 1970 Whitledge 1985

Massachusetts Buzzards Bay Documented 1980 Summer hypoxia. Whitledge 1985, 

Bricker et al. 2007, 

Buzzards Bay NEP 

2008

Massachusetts Clarks Cove None 1970 Whitledge 1985

Massachusetts New Bedford 

Harbor

Documented 1930 Loss of fishes and 

shellfish.

Low dissolved oxygen may 

have occurred in 1800s 

associated with whaling and 

textile industries, by 1930 

water quality poor.

Whitledge 1985, 

NOAA 2008

Massachusetts Tauton River Documented 1970 Whitledge 1985

New Jersey Barnegat Bay Documented 1980 Mass mortality of 

benthos with annual 

recolonization.

Whitledge 1985, 

Moser 1998

New Jersey Great Egg 

Harbor River

Documented 1980 Whitledge 1985, 

Glenn et al. 1996

New Jersey Inland Bays Concern 2000 Bricker et al. 2007

New Jersey Little Egg Inlet Documented 1970 Garlo et al. 1979

New Jersey Metedeconk 

River

None 1980 Whitledge 1985

New Jersey Mullica River 

Estuary

Documented 1990 Dissolved oxygen low in 

1980s, hypoxic in 1990s.

Whitledge 1985, 

Glenn et al. 1996

New Jersey Newark Bay Concern 1980 Whitledge 1985

New Jersey Passaic River Concern 1980 Whitledge 1985
132 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

New Jersey Raritan Bay Documented 1970 Some improvement in 

dissolved oxygen from 1990s 

to 2000s. Improved from 

nutrient management. 

Christensen and 

Packard 1976, 

Whitledge 1985, 

Bricker et al. 1999, 

2007

New Jersey Raritan River Documented 1970 Whitledge 1985

New Jersey Sandy Hook Bay None 1980 Whitledge 1985

New Jersey Toms River None 1980 Whitledge 1985

New Jersey TownsendHereford InletDocumented 1990 Glenn et al. 1996, 

2004

New Jersey Tuckahoe River None 1980 Whitledge 1985

New Jersey Wading River Concern 1980 Whitledge 1985

New York Arthur Kill Documented 1970 Whitledge 1985

New York Berger Basin Documented 1970 Rhoads et al. 2001

New York Carmans River Documented 1990 Diel hypoxia present at times. Zaikowski et al. 2008

New York East River Documented 1920 Decline in dissolved oxygen 

recorded in 1910-1930. Now 

dissolved oxygen improved 

from nutrient management.

Parker and O'Reilly 

1991, Whitledge 

1985

New York Flushing Bay Documented 1990 Rhoads et al. 2001

New York Gardiners Bay None 1980 Whitledge 1985

New York Grassy Bay Documented 1970 Areas anoxic in June-August. Rhoads et al. 2001, 

Bricker et al. 2007

New York Great South Bay Documented 1980 Improved, but tidal creeks 

periodically hypoxic between 

July and September. Diel 

hypoxia may occur.

Whitledge 1985, 

Bricker et al. 2007, 

Zaikowski et al. 2008

New York Hackensack Concern 1980 Whitledge 1985

New York Harlem River Documented 1970 Whitledge 1985

New York Hudson River Documented 1960 Recovered from low dissolved 

oxygen through nutrient 

management.

Bronsnan and O'Shea 

1996, Whitledge 

1985

New York Kill van Kull 

River

Documented 1970 Whitledge 1985

New York Long Island 

Sound

Documented 1970 Avoidance and 

some mortality of 

fishes. About 30% 

of Sound benthos 

impacted by 

hypoxia. 

Dissolved oxygen declined 

from 1990s to 2000s. Area 

of hypoxia has increased 

from 1980s. Hypoxic June 

to September; duration, 

frequency, spatial coverages all 

increased since 1987.

Howell and Simpson 

1994, Welsh et al. 

1994, Schimmel et 

al. 1999, Anderson 

and Taylor 2001, Lee 

and Lwiza 2007

New York Lower Bay Concern 1980 Whitledge 1985

New York Mill Basin Documented 1990 Avoidance by 

mobile fauna.

Rhoads et al. 2001

New York Mohawk River Concern 1980 Whitledge 1985

New York Narrows Documented 1970 Whitledge 1985, Lee 

and Lwiza 2007
Scientific Assessment of Hypoxia in U.S. Coastal Waters 133

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

New York New York Bight Documented 1970 Surf clam/

finfish mortality, 

Avoidance, 

northward migration 

of bluefish blocked. 

Mass mortality 

of benthos with 

multi-year recovery. 

Large economic 

losses.

Calm weather led to 

stratification and bloom of 

Ceratium tripos, one time 

event. May have involved 

upwelling on nutrient-rich 

water.

Segar and Berberian 

1976, Garlo et al. 

1979, Sindermann 

and Swanson 1980, 

Swanson and Parker 

1988, Figley et al. 

1979, Azarovitz et 

al. 1979, Boesch and 

Rabalais 1991

New York New York Bight 

Sewage Dump

Documented 1970 Summer hypoxia associated 

with sewage dump site, 10% 

saturation at center of dump 

site.

Segar and Berberian 

1976

New York New York City 

Harbor

Documented 1920 Stressed fishes. 

Mass mortality of 

benthos with annual 

recolonization.

Decline in dissolved oxygen 

recorded in 1910-1930. Now 

dissolved oxygen improved 

from nutrient management.

Parker and O'Reilly 

1991

New York Norton Basin Documented 1990 Avoidance by 

mobile fauna.

Rhoads et al. 2001

New York Patchogue River Documented 1990 Benthic species 

richness severely 

impacted.

Channelization induced 

stratification an important 

factor. Deep areas hypoxic 

year round.

Zaikowski et al. 2008

New York Shellbank Basin Documented 1990 Rhoads et al. 2001

New York Swan River Documented 1990 Benthic species 

richness moderately 

to severely 

impacted.

Channelization induced 

stratification an important 

factor. 

Zaikowski et al. 2008

New York Tivolie South Documented 1990 Sanger et al. 2002

New York Upper Bay Concern 1980 Whitledge 1985

Rhode Island Greenwich Bay Documented 2000 Fish kill in 2003. 0-4% of area <2.3 mg/l 

dissolved oxygen.

Deacutis et al. 2006, 

Melrose et al. 2007

Rhode Island Mount Hope Bay Documented 2000 0.5-2.5% of area <2.3 mg/l 

dissolved oxygen.

Deacutis et al. 2006, 

Melrose et al. 2007

Rhode Island Narragansett Bay Documented 1950 Reduced abundance 

or absence of 

benthos.

Hypoxic June to September, 

related to high nutrient loads. 

Hypoxia and anoxia present in 

1950s in upper part of bay, low 

dissolved oxygen widespread 

by 1980s. Dissolved oxygen 

declined from 1990s to 2000s.

Whitledge 1985, 

Bricker et al. 1999, 

2007, Melrose et al. 

2007, Bergondo et 

al. 2005, Deacutis et 

al. 2006, Cicchetti et 

al. 2006

Rhode Island Pettaquamscutt 

River

Documented 1990 Wilkin and Barnes 

1997

Rhode Island Potters Cove Documented 1990 Sanger et al. 2002

Rhode Island Providence River Documented 1980 Related to sewage discharges, 

27-39% of the river was <2.3 

mg/l dissolved oxygen.

Whitledge 1985, 

Bergondo et al. 2005, 

Deacutis et al. 2006, 

Melrose et al. 2007

Virginia Appomattox 

River

None 1990 CBP 2008

Virginia Back Bay None 1980 Whitledge 1985
134 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Virginia Chesapeake Bay, 

lower

Documented 1980 Lower benthic 

diversity, lower 

biomass, lower 

proportion of deepdwelling biomass 

at hypoxia-affected 

areas.

Dauer et al 1992

Virginia Chickahominy None 1990 CBP 2008

Virginia Chuckatuck 

River

None 1990 CBP 2008

Virginia Cobb Bay None 1980 Whitledge 1985

Virginia Corrotoman 

River

None 1990 CBP 2008

Virginia East River None 1990 CBP 2008

Virginia Elizabeth River, 

Eastern Branch

Documented 1990 CBP 2008

Virginia Elizabeth River, 

Southern Branch

Documented 1990 CBP 2008

Virginia Elizabeth River, 

Western Branch

Concern 1990 CBP 2008

Virginia Goodwin Island Documented 1990 Low dissolved oxygen in 

submerged aquatic vegetation 

bed.

Sanger et al. 2002

Virginia Grays Creek None 1990 CBP 2008

Virginia Hog Island Bay None 1980 Whitledge 1985

Virginia James River None 1980 Dissolved oxygen improved 

from nutrient management.

Whitledge 1985

Virginia Jones-Gilligan 

Creek

None 1990 CBP 2008

Virginia Lafayette River Concern 1990 CBP 2008

Virginia Lynnhaven Inlet None 1990 CBP 2008

Virginia Mattaponi River Documented 1990 CBP 2008

Virginia Mobjack Bay Documented 1990 CBP 2008

Virginia Mud Creek None 1990 CBP 2008

Virginia Nansemond 

River

Documented 1990 CBP 2008

Virginia North River None 1990 CBP 2008

Virginia Onancock Creek Documented 2000 Wang 2005

Virginia Pagan River None 1990 CBP 2008

Virginia Pamunkey River None 1990 CBP 2008

Virginia Paradise Creek None 1990 CBP 2008

Virginia Piankatank River None 1990 CBP 2008

Virginia Pocomoke Sound None 1980 Whitledge 1985

Virginia Poropotank 

River

None 1990 CBP 2008

Virginia Queen Creek None 1990 CBP 2008

Virginia Rappahannock 

River

Documented 1980 Avoidance by 

mobile fauna. 

Mortality of 

benthos with annual 

recolonization.

Some anoxia in summer. Llansó 1992, Kuo et 

al. 1991
Scientific Assessment of Hypoxia in U.S. Coastal Waters 135

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Virginia Robinson Creek None 1990 CBP 2008

Virginia Sarah Creek None 1990 CBP 2008

Virginia Scuffletown 

Creek

None 1990 CBP 2008

Virginia Severn Creek None 1990 CBP 2008

Virginia South Bay None 1980 Whitledge 1985

Virginia Taskinas Creek Documented 1990 Sanger et al. 2002

Virginia Timberneck 

Creek

None 1990 CBP 2008

Virginia Totuskey Creek None 1990 CBP 2008

Virginia Urbanna Creek None 1990 CBP 2008

Virginia Ware River None 1990 CBP 2008

Virginia Warwick River None 1990 CBP 2008

Virginia Weeks Creek None 1990 CBP 2008

Virginia Willoughby Bay None 1990 CBP 2008

Virginia York River Documented 1970 Avoidance by 

mobile fauna with 

reduced diversity 

following low 

dissolved oxygen 

events. Little to 

no response in the 

benthos.

Hypoxia associated with 

spring-neap tidal cycle.

Haas 1977, Pihl et al. 

1991, 1992, Diaz et 

al. 1992, Sagasti et al 

2001, 2003, Seitz et 

al. 2003

Northeast Region

Maine Androscoggin 

River

None 1980 Whitledge 1985, 

Bricker et al. 2007

Maine Blue Hill Bay None 1980 Whitledge 1985

Maine Casco Bay None 1980 Whitledge 1985, 

Bricker et al. 2007

Maine Cobscook Bay None 1980 Whitledge 1985

Maine Damariscotta 

River 

None 1980 Whitledge 1985

Maine Englishman Bay None 1980 Whitledge 1985

Maine Fore River None 1980 Whitledge 1985

Maine Frenchman Bay None 1980 Whitledge 1985

Maine Great Bay Concern 2000 Evidence of decline in 

dissolved oxygen levels.

Bricker et al. 2006

Maine Kennebec River None 1980 Whitledge 1985

Maine Machias Bay None 1980 Whitledge 1985

Maine Machias River 

Estuary

None 1980 Whitledge 1985

Maine Muscongus Bay None 1980 Whitledge 1985

Maine Narraguagus Bay None 1980 Whitledge 1985

Maine Narraguagus 

River

Concern 1980 Whitledge 1985

Maine Passamaquoddy 

Bay

None 1980 Whitledge 1985

Maine Penobscot Bay/

River 

None 1980 Whitledge 1985

Maine Pleasant Bay None 1980 Whitledge 1985

Maine Saco Bay None 1980 Whitledge 1985
136 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Maine Sheepscot Bay None 1980 Whitledge 1985

Maine St. Croix River None 1980 Whitledge 1985

Maine Wells Bay Documented 1990 Sanger et al. 2002

Maine Wells Inlet Documented 1990 Daily cycle of dissolved 

oxygen from supersaturated to 

hypoxic, Submerged aquatic 

vegetation bed.

Sanger et al. 2002

Maine Wohoa Bay None 1980 Whitledge 1985

Massachusetts Boston Harbor None 1980 Entire region recovered from 

low dissolved oxygen through 

nutrient management.

Whitledge 1985, 

Bricker et al. 1999, 

2007, Diaz et al. 

2008

Massachusetts Cape Cod Bay Documented 1990 Blooms. Whitledge 1985, 

Rabalais 1998

Massachusetts Charles River Documented 1980 Taylor 2000

Massachusetts Dorchester Bay Documented 1980 Had poor water quality in 

1980s. Low dissolved oxygen 

in 1980s now improved from 

nutrient management.

Maciolek et al. 2005, 

Diaz et al. 2008

Massachusetts Duxbury Bay None 1980 Whitledge 1985

Massachusetts Fore River Documented 1980 Neponset River 

Watershed 

Association 2004

Massachusetts Herring River Documented 1980 Fish kills, decline of 

alewife fishery.

Anoxia, 1-3 weeks. Portnoy 1991

Massachusetts Massachusetts 

Bay

None 1990 Bricker et al. 2007

Massachusetts Merrimack River Documented 1970 Whitledge 1985

Massachusetts Plum Island 

Sound

None 1990 Rabalais 1998, 

Bricker et al. 2007

Massachusetts Waquoit Bay Documented 1990 Daily cycle of dissolved 

oxygen from saturated to 

hypoxic.

Fritz et al. 1996, 

D'Avanzo and 

Kremer 1994, 

Bricker et al. 2007

New 

Hampshire

Great Bay Documented 1980 Whitledge 1985, 

Bricker et al. 2007

New 

Hampshire

Hampton Harbor 

Estuary

None 1990 Rabalais 1998

New 

Hampshire

Piscataqua River None 1980 Whitledge 1985, 

Bricker et al. 2007

South Atlantic Region

Florida Amelia River Documented 1970 Windsor 1985

Florida Banana River Concern 1980 Windsor 1985
Scientific Assessment of Hypoxia in U.S. Coastal Waters 137

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Florida Biscayne Bay Documented 1970 Related to releases of 

freshwater from canals. 

Dissolved oxygen declined 

from 1990s to 2000s.

Bricker et al. 1999, 

2007, Windsor 1985, 

Leverone 1995

Florida Canal 17 Documented 1980 Whitledge 1985

Florida Cedar Creek Documented 1980 Windsor 1985

Florida East Holloway 

Canal

Documented 1980 Windsor 1985

Florida Eau Gallie 

Harbor

Concern 1980 Whitledge 1985

Florida Gulf and West 

Canals

Documented 1980 Windsor 1985

Florida Halifax River Documented 1980 Windsor 1986

Florida Haw Creek Documented 1980 Windsor 1985

Florida Hillsboro Canal Documented 1980 Windsor 1985

Florida Indian River Documented 2000 Improvement in dissolved 

oxygen levels from 1990s to 

2000s.

Bricker et al. 1999, 

2007, Windsor 1985

Florida Lofton Creek Concern 1980 Windsor 1985

Florida Loxahatchee 

River

Concern 1980 Windsor 1985

Florida Matanzas River Concern 1980 Windsor 1985

Florida Miami Canal Documented 1980 Windsor 1985

Florida Mosquito 

Lagoon

Concern 1980 Windsor 1985

Florida Naples Bay Documented 1980 Windsor 1985

Florida Nassau River None 1980 Windsor 1985

Florida North and South 

New River 

Canals

Documented 1980 Windsor 1985

Florida North River Documented 1980 Windsor 1987

Florida Ortega River Documented 1980 Windsor 1985

Florida Pottsburg Creek Documented 1980 Windsor 1985

Florida Ribault River Documented 1980 Windsor 1985

Florida Rice Creek Documented 1980 Windsor 1985

Florida Sebastian Creek Documented 1980 Windsor 1985

Florida Sisters Creek Concern 1980 Windsor 1985

Florida South Amelia 

River

Concern 1980 Windsor 1985

Florida South Relief 

Canal

Documented 1980 Windsor 1985

Florida Spruce Creek None 1980 Windsor 1985

Florida St. Johns River Documented 1970 Mortality of 

benthos, massive 

fish kills with 

unknown cause, 

may be multiple 

stressors.

Windsor 1985, 

Mason 1998

Florida St. Lucie Canal Concern 1980 Windsor 1985
138 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Florida St. Lucie River Documented 1980 Chamberlain and 

Hayward 1996, 

Windsor 1985

Florida St. Marys River Documented 1970 Anoxia develops in 

summer.

No significant declining trend 

in dissolved oxygen from 

1960s to 2000s

Windsor 1985, Verity 

et al. 2006

Florida Sykes Creek Documented 1980 Windsor 1985

Florida Tenmile Creek Documented 1980 Windsor 1985

Florida Tolomato River Concern 1980 Windsor 1985

Florida Tomoka River Concern 1980 Windsor 1985

Florida Trout River Documented 1980 Windsor 1985

Florida Turkey Creek Documented 1980 Windsor 1986

Florida West Palm Beach 

Canal

Documented 1980 Windsor 1985

Florida Whitewater Bay Concern 1980 Windsor 1985

Georgia Altamaha Sound Concern 2000 Declining trend in dissolved 

oxygen related to nutrient 

loadings. No hypoxia in 

1980s.

Stanley 1985, Verity 

et al. 2006

Georgia Altamaha River Documented 2000 Significant declining trend in 

dissolved oxygen from 1970s 

to 2000s. No hypoxia in 

1980s.

Stanley 1985, Verity 

et al. 2006

Georgia Brunswich River Concern 1970 Stanley 1985

Georgia Brunswick 

Harbor

Concern 1970 Stanley 1985

Georgia Cumberland 

Sound

Documented 2000 Declining trend in Dissolved 

oxygen related to nutrient 

loadings.

Stanley 1985, Verity 

et al. 2006

Georgia Doboy Sound None 1980 Stanley 1985

Georgia Duplin River Documented 1970 Daily cycle of dissolved 

oxygen from supersaturated to 

hypoxic.

Frankenberg 1976, 

Stanley 1985

Georgia Medway River None 1970 Stanley 1985

Georgia Ogeechee River Documented 2000 Significant declining trend in 

dissolved oxygen from 1960s 

to 2000s. No hypoxia in 1970s.

Stanley 1985, Verity 

et al. 2006

Georgia Ogeechee Sound Concern 2000 Declining trend in dissolved 

oxygen related to nutrient 

loadings.

Stanley 1985, Verity 

et al. 2006

Georgia Ossabaw Sound Documented 1980 Related to organic matter 

washing out of swamps and 

marshes. Dissolved oxygen 

declined from 1990s to 2000s.

Stanley 1985, 

Bricker et al. 1999, 

2007

Georgia Sapelo Island Documented 2000 Daily cycle of dissolved 

oxygen from supersaturated to 

hypoxic.

Sanger et al. 2002

Georgia Sapelo Sound Concern 1990 No hypoxia in 1980s, declining 

trend is dissolved oxygen for 

2000s.

Stanley 1985, Verity 

et al. 2006
Scientific Assessment of Hypoxia in U.S. Coastal Waters 139

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Georgia Satilla River Documented 2000 Significant declining trend in 

dissolved oxygen from 1960s 

to 1990s. Not hypoxic in 

1970s.

Stanley 1985, Verity 

et al. 2006

Georgia Savannah River Documented 1980 Nonpoint sources a factor. 

Significant declining trend in 

dissolved oxygen from 1960s 

to 2000s.

Stanley 1985, Verity 

et al. 2006, Bricker et 

al. 2007

Georgia Skidaway River 

Estuary

Concern 1990 High rate of microbial 

respiration causes low 

dissolved oxygen despite 

strong vertical and horizontal 

mixing. Declining trend in 

dissolved oxygen related to 

nutrient loadings.

Verity et al. 2006, 

Bricker et al. 2007

Georgia St. Andrews 

Sound

Concern 1990 No hypoxia in 1980s, declining 

trend is dissolved oxygen for 

2000s.

Stanley 1985, Verity 

et al. 2006

Georgia St. Catherine 

Sound

None 1980 Stanley 1985

Georgia St. Marys River Concern 1970 Stanley 1985

Georgia St. Simons 

Sound

None 1980 Stanley 1985, 

Rabalais 1998, 

Bricker et al. 2007

Georgia Turtle River Documented 1970 Stanley 1985

Georgia Tybee Creek None 1970 Stanley 1985

Georgia Wassaw Sound None 1980 Stanley 1985

Georgia Wilmington 

River

None 1970 Stanley 1985

North Carolina Ace Basin Documented 1990 Sanger et al. 2002

North Carolina Albemarle Sound Documented 1970 Mortality of benthos 

and mobile fauna.

Hurricane increased freshwater 

and nutrient input. Hypoxia 

has worsened in 2000s.

Stanley 1985, 

Bricker et al. 1999, 

2007, Paerl et al. 

2000

North Carolina Alligator River None 1980 Stanley 1985

North Carolina Barnards Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Black River Documented 1990 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Bogue Sound Concern 1980 Stanley 1985

North Carolina Browns Creek Concern 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Cape Fear River Documented 1970 Fish kills, reduced 

benthos.

Stanley 1985, Mallin 

et al. 1999, 2006, 

Posey et al. 1999

North Carolina Carolina Beach 

Lake

Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Chowan River Documented 1980 Stanley 1985
140 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

North Carolina Colly Creek Concern 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Core Sound None 1980 Stanley 1985

North Carolina Currituck Sound None 1980 Stanley 1985

North Carolina Dutchman Creek Concern 1970 Stanley 1985

North Carolina Futch Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

MacPherson et al. 

2007, Mallin et al. 

2006

North Carolina Great Coharie 

Creek

Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Hammond Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Hewletts Creek Documented 2000 Heavily developed watershed. MacPherson et al. 

2007, Mallin et al. 

2006

North Carolina Little Coharie 

Creek

Concern 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Little River None 1980 Stanley 1985

North Carolina Masonboro Inlet Documented 1990 Sanger et al. 2002

North Carolina Motts Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Neuse River 

Estuary

Documented 1980 Fish kills, mortality 

of oyster. Reduced 

prey abundance 

and habitat quality 

for fish. Mortality 

of benthos 

with decreased 

abundance.

Hypoxia may have developed 

earlier based on Macoma

populations. Improvement in 

dissolved oxygen from 1990s 

to 2000s.

Paerl et al. 1995, 

1998, Lenihan and 

Peterson 1998, 

Lenihan 1999, 

Whitledge 1985, 

Buzzelli et al. 2002, 

Bishiop et al. 2006, 

Bell and Eggleston 

2005, Baird et al. 

2004, Aumann et al. 

2006, Powers et al. 

2005

North Carolina New River Documented 1980 Stanley 1985, 

Bricker et al. 2007

North Carolina Newport River None 1980 Stanley 1985

North Carolina North River None 1980 Stanley 1985

North Carolina Northeast Cape 

Fear River

Documented 1990 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Pages Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

MacPherson et al. 

2007, Mallin et al. 

2006
Scientific Assessment of Hypoxia in U.S. Coastal Waters 141

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

North Carolina Pamlico River Documented 1960 Mortality of fishes, 

mass mortality 

of benthos, low 

macrobenthic 

diversity and 

density in summer, 

recolonization by 

winter.

Stanley 1985, Tenore 

1972, Hobbie et al. 

1975, Stanley and 

Nixon 1992

North Carolina Pamlico Sound Documented 1990 Common finfish 

species (pinfish, 

spot, croaker) had 

skin lesions and 

signs of systemic 

bacterial infections.

No hypoxia in 1960s through 

the 1980s, low dissolved 

oxygen developed in late 

1990s. Hurricane increased 

freshwater and nutrient input.

Paerl et al. 2000, 

Stanley 1985

North Carolina Pasquotank 

River

None 1980 Stanley 1985

North Carolina Perquimans 

River

None 1980 Stanley 1985

North Carolina Pungo River None 1980 Stanley 1985

North Carolina Six Runs Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina Smith Creek Documented 2000 Combination of agricultural, 

urban, suburban runoff 

contribute to nutrient loading.

Mallin et al. 2006

North Carolina White Oak River None 1980 Stanley 1985

South Carolina Ashley River None 1980 Stanley 1985

South Carolina Beresford Creek Documented 1990 Lerberg et al. 2000

South Carolina Broad River Documented 2000 Dissolved oxygen improved 

from 1990s to 2000s.

Bricker et al. 1999, 

2007

South Carolina Bull Creek Documented 1990 Lerberg et al. 2000

South Carolina Bulls Bay None 1980 Stanley 1985

South Carolina Charleston 

Harbor

Documented 2000 Improved wastewater 

treatment, phosphate ban. 

Improvement in dissolved 

oxygen from 1990s to 2000s.

Bricker et al. 1999, 

2007, Windsor 1985

South Carolina Combahee River None 1980 Stanley 1985

South Carolina Cooper River Concern 1980 Whitledge 1985

South Carolina Coosaw River None 1980 Stanley 1985

South Carolina Copper River Concern 1980 Stanley 1985

South Carolina Deep Creek Documented 1990 Lerberg et al. 2000

South Carolina Diesel Creek Documented 1990 Lerberg et al. 2000

South Carolina Foster Creek Documented 1990 Lerberg et al. 2000

South Carolina James Island 

Creek

Documented 1990 Avoidance by fishes, 

mortality of benthos.

Burnett 1997

South Carolina Kiawah River None 1980 Stanley 1985

South Carolina Little River Inlet None 1980 Stanley 1985
142 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

South Carolina Long Bay Documented 2000 Mortality of 

flounder.

Recently documented hypoxia 

may be related to multiple 

factors including high 

chlorophyll a levels.

Koepfler et al. 2007

South Carolina Malind Creek Documented 2000 Gillett et al. 2005

South Carolina Murrells Inlet None 1980 Stanley 1985

South Carolina New Market 

Creek

Documented 1990 Lerberg et al. 2000

South Carolina North Edisto 

River

Concern 1980 Stanley 1985, 

Bricker et al. 2007

South Carolina North Inlet Documented 2000 Stanley 1985, Sanger 

et al. 2002

South Carolina North Santee 

River

None 1980 Stanley 1985

South Carolina Okatee Creek Documented 2000 Gillett et al. 2005

South Carolina Orange Grove 

Creek

Documented 1990 Lerberg et al. 2000

South Carolina Pee Dee River Concern 1980 Stanley 1985

South Carolina Port Royal 

Sound

None 1980 Stanley 1985

South Carolina Rathall Creek Documented 1990 Lerberg et al. 2000

South Carolina Santee River Concern 1990 Rabalais 1998, 

Bricker et al. 2007

South Carolina Shem Creek Documented 1990 Lerberg et al. 2000

South Carolina South Atlantic 

Bight

Concern 1970 Dissolved oxygen around 3 

mg/l at 100 m depth in 1973-

74.

Stanley 1985

South Carolina South Edisto 

River

None 1980 Stanley 1985

South Carolina South Santee 

River

None 1980 Stanley 1985

South Carolina St. Helena Sound Documented 1980 Stanley 1985, 

Bricker et al. 2007

South Carolina Stono River Documented 1990 No hypoxia in 1980s, low 

dissolved oxygen developed in 

1990s.

Stanley 1985, 

Bricker et al. 1999, 

2007

South Carolina Wando River Concern 1980 Stanley 1985, 

Whitledge 1985

South Carolina Winyah Bay Documented 1980 Stanley 1985, 

Bricker et al. 2007

Pacific Coast Region and Hawaii

Alaska Ward Cove Documented 1950 Periodic fish kill in 

1950s.

Related to pulp mill discharge 

1954-1997, circulation is pore 

in cove, dissolved oxygen still 

low in areas.

Karna 2003

California Alamitos Bay Documented 2000 Rabalais 1998

California Anaheim Bay to 

Balsa Chica

Concern 1990 Rabalais 1998

California Azevedo Pond Documented 1990 Diel cycling, low dissolved 

oxygen related to high primary 

production.

Beck and Bruland 

2000
Scientific Assessment of Hypoxia in U.S. Coastal Waters 143

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

California Big Lagoon Documented 1980 Collias 1985, Engle 

et al. 1999

California Coyote Creek Documented 1970 Fisherman 

reported absence 

of fish and pelagic 

invertebrates, 

fish returned after 

hypoxia ended.

Sewage spill. Cloern and Oremland 

1983

California Drakes Estero None 1980 Collias 1985

California Eel River None 1990 Rabalais 1998, 

Bricker et al. 2007

California Elkhorn Slough Documented 1990 Dissolved oxygen improved 

from 1990s to 2000s.

Bricker et al. 1999, 

2007, Sanger et al. 

2002

California Elkhorn Slough, 

Upper Pond

Documented 2000 Bricker et al. 1999, 

2007, Sanger et al. 

2002

California Humboldt Bay/

Arcata Bay

None 1980 Collias 1985

California Klamath River None 1990 Rabalais 1998, 

Bricker et al. 2007

California Long Beach 

Harbor

Documented 1960 Whitledge 1985

California Los Angeles 

Harbor

Documented 1950 Mass mortality of 

benthos with multiyear recovery.

Improved from nutrient 

management.

Reish 1955, 2000

California Mission Bay None 1990 Rabalais 1998, 

Bricker et al. 2007

California Monteray Bay Documented 2000 Combination of anthropogenic 

and natural factors.

Okey 2003

California Morro Bay None 1990 Rabalais 1998, 

Bricker et al. 2007

California Newport Bay Documented 1980 Dissolved oxygen improved 

from 1990s to 2000s.

Collias 1985, 

Rabalais 1998

California North San 

Francisco Bay 

Estuary

Documented 2000 Fish Kill Anoxia develops. Lehman et al. 2004

California Palos Verde 

Shelf

None 1970 Organic content of sediment 

enriched from sewage, but no 

hypoxia.

Smith et al. 2001, 

Weisberg (Personal 

Communication)

California San Diego Bay Documented 1980 Collias 1985, 

Rabalais 1998

California San Francisco 

Bay North

Concern 1980 Collias 1985

California San Francisco 

Bay South

Documented 1960 Hypoxia eliminated with 

sewage treatment plants. 

Recovered from low dissolved 

oxygen through nutrient 

management.

Nichols et al. 1986, 

Bricker et al. 2007
144 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

California San Joaquin 

River

Documented 1960 Salmon migration 

blocked when 

dissolved oxygen <6 

mg/l. High bacterial 

respiration and 

nitrification make 

dissolved oxygen 

low, stratification is 

weak.

Sewage discharge and 

nonpoint runoff are sources 

of organic matter, primary 

production also contributes. 

First <2 mg/l dissolved oxygen 

in 1972.

Lehman et al. 2004, 

Bricker et al. 2007, 

Jassby and Van 

Nieuwenhuyse 2005

California San Pedro Bay None 1990 Rabalais 1998, 

Bricker et al. 2007

California Santa Monica 

Bay

Documented 1990 Rabalais 1998, 

Bricker et al. 2007

California Smith River None 1980 Collias 1985

California Tijuana Estuary Documented 2000 Dissolved oxygen improved 

from 1990s to 2000s.

Bricker et al. 2007, 

Sanger et al. 2002

California Tomales Bay/

Bodega Harbor

Concern 1980 Collias 1985

Hawaii O'ahu, Off 

Southern Shore

Documented 2000 Mortality of benthos 

with low species 

richness and 

abundance.

Fish aquaculture. Lee et al. 2006

Oregon Alsea River None 1980 Collias 1985

Oregon California 

Current System

Documented 2000 Mortality of fishes 

and mass mortality 

of benthos.

Shifting wind patterns lead 

to extensive shallow shelf 

hypoxia. Related to upwelling 

and phytoplankton bloom. 

Hypoxia developed on inner 

shelf in 2000s.

Grantham et al. 2004, 

Chan et al. 2008

Oregon Columbia River None 1980 Collias 1985, Keefer 

et al. 2008

Oregon Coos Bay None 1980 Collias 1985

Oregon Coquille River None 1980 Collias 1985

Oregon Nehalem River None 1980 Collias 1985

Oregon Nestucca Bay None 1980 Collias 1985

Oregon Netarts Bay None 1980 Collias 1985

Oregon Rogue River Documented 1980 Collias 1985, Sanger 

et al. 2002

Oregon Siletz Bay None 1980 Collias 1985

Oregon Siuslaw River None 1980 Collias 1985

Oregon South Slough Documented 1990 Daily cycle of dissolved 

oxygen from supersaturated to 

hypoxic.

Sanger et al. 2002

Oregon Tillamook Bay None 1980 Collias 1985

Oregon Umpqua River Concern 1970 1970s intrusion of low 

dissolved oxygen (<2 mg/l). 

No hypoxia in 1980s.

Collias 1985, Brown 

et al. 2007

Oregon Yaquina Bay Documented 2000 No hypoxia in 1980s. Low 

dissolved oxygen water at 

times advected into estuary 

from shelf.

Collias 1985, Brown 

et al. 2007
Scientific Assessment of Hypoxia in U.S. Coastal Waters 145

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Washington Admiralty Inlet Concern 1990 Washington State 

Dept. Ecol. 2002

Washington Bellingham Bay Concern 1990 No hypoxia in 1980s. Collias 1985, 

Washington State 

Dept. Ecol. 2002

Washington Budd Inlet Documented 1980 Whitledge 1985, 

Washington State 

Dept. Ecol. 2002

Washington Commencement 

Bay

Concern 1990 Washington State 

Dept. Ecol. 2002

Washington Dana Passage None 1990 Washington State 

Dept. Ecol. 2002

Washington Discovery Bay Documented 1990 Washington State 

Dept. Ecol. 2002

Washington DRA002 None 1990 Washington State 

Dept. Ecol. 2002

Washington ELD002 None 1990 Washington State 

Dept. Ecol. 2002

Washington Elliott Bay Documented 1990 Washington State 

Dept. Ecol. 2002

Washington GOR001 None 1990 Washington State 

Dept. Ecol. 2002

Washington Grays Harbor Concern 1980 Collias 1985

Washington Hood Canal Documented 1930 Fish did not enter 

dissolved oxygen 

minimum later in 

water column while 

invertebrates did.

Dissolved oxygen declined 

from 1990s to 2000s.

Paulson et al. 1993, 

Bricker et al. 2007, 

Parker-Stetter and 

Horne 2008

Washington Lynch Cove Documented 1980 Low dissolved oxygen all year 

round.

Whitledge 1985, 

Washington State 

Dept. Ecol. 2002

Washington Oakland Bay None 1990 Washington State 

Dept. Ecol. 2002

Washington Padilla Bay Documented 1990 No hypoxia in 1980s, Low 

dissolved oxygen in submerged 

aquatic vegetation bed.

Collias 1985, Sanger 

et al. 2002

Washington Penn Cove Documented 2000 Washington State 

Dept. Ecol. 2002

Washington POD007 None 1990 Washington State 

Dept. Ecol. 2002

Washington Port Gamble Concern 1990 Washington State 

Dept. Ecol. 2002

Washington Port Gardner None 1980 Collias 1985

Washington Port Orchard 

System

Concern 1980 Collias 1985

Washington Port Susan Documented 1980 Collias 1985

Washington Possession 

Sound

Concern 1990 Washington State 

Dept. Ecol. 2002

Washington Puget Sound None 1990 Rabalais 1998, 

Bricker et al. 2007

Washington Samish Bay Concern 1980 No hypoxia in 1980s. Collias 1985

Washington Saratoga Passage Documented 1990 Washington State 

Dept. Ecol. 2002
146 Scientific Assessment of Hypoxia in U.S. Coastal Waters

Appendix III. Table of Systems

State System Condition

Decade 

Condition 

First

Recorded

Faunal

Response

Trends and Other

Comments Reference

Washington Sequim/

Discovery Bays

Documented 1980 Collias 1985

Washington Sinclair Inlet Concern 1990 Washington State 

Dept. Ecol. 2002

Washington Skagit Bay Documented 1990 Rabalais 1998

Washington South Puget 

Sound

Documented 1980 Collias 1985

Washington Straight of 

Georgia

Concern 1990 Washington State 

Dept. Ecol. 2002

Washington TOT001 None 1990 Washington State 

Dept. Ecol. 2002

Washington West Point Documented 1990 Washington State 

Dept. Ecol. 2002

Washington Whidbey Basin Documented 1980 Collias 1985, 

Rabalais 1998

Washington Willapa Bay None 1980 Collias 1985

Washington Willapa River Documented 1990 Washington State 

Dept. Ecol. 2002

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