Through A Fish’s Eye:

The Status of Fish Habitats 

in the United States

2010
Executive Summary 1

Foreword 3

How to Read and Understand This Report 4

National Overview 7

Northeastern States (ME, NH, VT, NY, MA, RI, CT) 9

Mid-Atlantic States (PA, NJ, WV, VA, MD, DE) 12

Southeast Atlantic States (NC, SC, GA) 15

Upper Midwest States (MN, WI, MI) 18

Central Midwest States (IA, IL, IN, OH) 21

Central Mississippi River States (MO, AR, KY, TN) 24

Focus on the Gulf of Mexico 27

Eastern Gulf of Mexico States (LA, MS, AL, FL) 29

Southern Plains States (KS, OK, TX) 32

Northern Plains States (ND, SD, NE) 35

Mountain States (CO, ID, MT, UT, WY) 38

Southwestern States (AZ, NV, NM) 41

Pacific Coast States (WA, OR, CA) 44

Alaska 47

Hawaii 50

Marine Waters 53

Challenges and Opportunities 60

Methodology 63

Suggestions for Further Reading 66

Acknowledgements 68

Fish and fishing are integral to the American story. Salmon have sustained 

Native Americans for centuries. Shad and cod helped the early European 

colonists survive and were critical trade commodities. However, the tide 

has turned, and the waters fish inhabit are less able to support them due 

to effects of human activities. The fish need our help to protect and restore 

the places where they live. While thousands of projects have improved 

fish habitat on a small scale throughout the United States in the past three 

decades, gains have been outpaced by continuing human impacts on the 

landscape. The need for action has never been greater. Together we can 

ensure that future generations will be able to enjoy clean and healthy 

streams, lakes, estuaries, and oceans teeming with fish. 

Contents

We have seen Indians in immense 

numbers, and all those on this 

coast of the Pacific contrive to make 

a good subsistence on various seeds, 

and by fishing.” – Junipero Serra

“ May the holes in your 

net be no larger than 

the fish in it.” – Irish Blessing

T “ he charm of fishing is that it is 

the pursuit of what is elusive 

but attainable, a perpetual series 

of occasions for hope.” 

– John Buchan 

“

This report should be cited as: National Fish Habitat Board, 2010. Through a Fish’s Eye: The Status of Fish Habitats in the United States 2010. Association of Fish and Wildlife Agencies, Washington D.C. 68 pp.
1

The United States is home to a diverse array of freshwater and marine 

fish, shellfish, and other aquatic species. More than 3,000 species 

of fish inhabit America’s streams, rivers, lakes, reservoirs, marshes, 

swamps, bays, estuaries, coral reefs, seagrass beds, shallow water banks, deep 

ocean canyons, and other watery habitats. The United States is also home to 

over 300 million people, all depending on the same water that fish depend 

upon. 

Healthy habitats are essential for sustainable fish populations. Unfortunately, 

in many places around the United States, fish and the habitats on which they 

depend are in decline. Almost 40 percent of the nation’s freshwater fish species 

are considered at risk or vulnerable to extinction. Habitat loss is the most 

common cause for extinction of freshwater fish in the United States over the 

past century, and many saltwater fish are also in decline due to habitat degradation. In 1997, Congress declared that one of the greatest long-term threats to 

the viability of commercial and recreational fisheries is the continuing loss of 

marine, estuarine, and other aquatic habitats.

This report summarizes the results of an unprecedented nationwide assessment 

of human effects on fish habitat in the rivers and estuaries of the United States. 

The assessment assigns watersheds and estuaries a risk of current habitat degradation ranging from very low to very high. These results allow comparison 

of aquatic habitats across the nation and within 14 sub-regions. The results 

also identify some of the major sources of habitat degradation. Unfortunately, 

not all sources of habitat degradation could be assessed, so some important 

factors such as small dams and abandoned mines could not be incorporated. 

Marine waters, lakes, and reservoirs were not assessed due to resource and data 

constraints, so previously published information was used to describe the 

condition of these fish habitats. Future revisions to the assessment will incorporate the missing data to the extent it is available.

Within the United States, areas of high risk and low risk of current habitat 

degradation occur in some discernable patterns. Urban corridors, regions with 

high-intensity agriculture, and locations of heavy industrial use correspond to 

some of the areas with a very high risk of current habitat degradation. Areas 

with a very low risk of current habitat degradation include regions with sparse 

populations and the lands and waters of national parks and other protected 

areas.

East of the Mississippi River, areas with the lowest risk of current habitat degradation occur principally in northern Maine and the northern Great Lakes area, 

as well as in sparsely populated parts of the Appalachian Mountain region. 

Areas with the highest risk of current habitat degradation occur in and around 

the heavily populated corridor from New York City to Washington D.C., 

including Long Island Sound and the Chesapeake Bay. Urbanization is a major 

factor in fish habitat degradation in this area, as is pollution, particularly excess 

nutrients. Areas with a very high or high risk of current habitat degradation 

Executive Summary
Steve Brown, WV DNR

Kip Evans, NOAA

2

due to agriculture occur in southern Florida, along the lower Mississippi River, 

and in the corn belt of Ohio, Illinois, and Indiana. 

In the upper and central midwest states as well as Oklahoma and Texas, areas 

with a low risk of current habitat degradation occur principally in southwest 

Texas and northeast Minnesota. Urbanization and ranching are responsible 

for large areas with a very high risk of habitat degradation in eastern Texas. 

Row crops contribute to areas with a high and very high risk of current habitat 

degradation in southern Minnesota, Iowa, Indiana, and western Arkansas. 

Corpus Christi Bay and some other Texas estuaries have a very high risk of 

current habitat degradation due to polluted runoff from urban areas.

In the western mountains, deserts, and coastal areas, large areas with a low 

risk of current habitat degradation are interspersed with areas of high risk due 

to urbanization (California, Arizona, and Colorado), intensive row crops and 

ranching (Idaho, California’s Central Valley, and southeast Washington), and 

alterations to water flow on the area’s rivers such as the Columbia, Snake, and 

Colorado Rivers. Because the assessment was not able to incorporate the effects 

of water withdrawals or culverts, habitats in this irrigation-dependent region 

may be more degraded than the assessment suggests. Estuaries in southern 

California and some parts of Hawaii have a high risk of current habitat degradation due to pollution from fast-growing coastal urban areas. Alaska has the 

largest areas with a very low risk of current habitat degradation, but urbanization, forestry, and road crossings are responsible for localized areas with an 

elevated risk of current habitat degradation.

Marine habitats of the United States generally are most productive near the 

coasts, which is also where they are most likely to become degraded by human 

activity. Major threats to marine habitat include pollution; damage to bottom 

habitat from dredging, fishing gear, or other activities; invasive species; marine 

debris; and climate change. 

This report provides an important picture of the challenges and opportunities 

facing fish and those engaged in fish habitat conservation efforts. Urbanization, 

agriculture, dams, culverts, pollution, and other human impacts have resulted 

in specific areas of degraded habitat where restoration is most likely needed 

to bring back the healthy habitats and fishing opportunities that once existed. 

Addressing degraded habitat also requires reducing or eliminating the sources 

of degradation mentioned in this report, through best management practices, 

land use planning, and engaging landowners, businesses, and local communities in the effort. This report identifies areas where those efforts are most 

needed. The report also points to areas where fish habitat is most likely still 

intact and should be protected to maintain its value for fish and other aquatic 

organisms. Resources for fish habitat conservation are limited, especially 

for the next few years. This report 

illustrates the need for strategic use 

of those existing resources through 

partnerships — such as the Fish 

Habitat Partnerships established 

under the National Fish Habitat 

Action Plan — that can identify 

the most effective use of funds and 

help the nation as a whole make 

progress in fish habitat conservation.
3

Foreword

Healthy waterways and thriving fish populations are vital to the 

well-being of American society, providing clean water, food, and 

recreation. They are important for less tangible reasons as well, 

as anyone who has fished a tranquil stream or paddled a salty bay can attest. 

Healthy waters sustain their ecological functions and resilience while meeting 

the social and economic needs of human society.

Unfortunately, in many places around the United States, fish and the habitats 

on which they depend are in decline. This is a particular concern to the 48 

million recreational anglers who pursue fish and to many others who depend 

upon fish and shellfish for sustenance and commerce. Revenue from recreational and commercial fisheries added more than $125 billion to our nation’s 

economy in 2006 (the latest year for which data are available). Almost 40 

percent of the nation’s freshwater fish species are considered at risk or vulnerable to extinction. Habitat loss is the most common cause for extinction of 

freshwater fish in the United States over the past century. Many saltwater fish 

are also in decline due to habitat degradation; Congress declared in 1997 that 

one of the greatest long-term threats to the viability of commercial and recreational fisheries is the continuing loss of marine, estuarine, and other aquatic 

habitats. 

Galvanized into action by continuing losses of aquatic habitat, an unprecedented coalition of anglers, conservation groups, scientists, state and federal 

agencies, and industry leaders forged the National Fish Habitat Action Plan in 

2006. The Action Plan is an investment strategy for making the most effective 

use of habitat conservation dollars and achieving real gains in aquatic habitat 

quality and quantity by protecting, restoring, and enhancing key fisheries 

habitats.

The objectives of the Action Plan are to:

Conduct a condition analysis of all fish habitats within the United States 

by 2010.

Prepare a “Status of Fish Habitats in the United States” report in 2010 and 

every 5 years thereafter.

Identify priority fish habitats and establish Fish Habitat Partnerships 

targeting these habitats by 2010. 

Establish 12 or more Fish Habitat Partnerships throughout the United 

States by 2010.

Protect all intact and healthy fish habitats by 2015.

Improve the condition of 90 percent of priority habitats and species 

targeted by Fish Habitat Partnerships by 2020.

This report and the assessments upon which it was based were developed to 

meet the first two objectives of the Action Plan. The second two objectives 

have been met through the establishment of 17 Fish Habitat Partnerships 

throughout all 50 states. Fish Habitat Partnerships involve diverse groups 

of public and private partners with 

common interests in fish habitat conservation. Examples of their work are highlighted throughout this report. These 

efforts are part of a larger strategy that, 

through the joint efforts of regional and 

national partners, will result in measurable and sustained improvement in the 

condition of priority fish habitat in the 

United States.

Fish habitat provides the 

foundation for healthy 

fish populations. Habitat 

refers to the chemical, 

physical, and biological 

conditions that fish require 

throughout their lives.
NOAA

This report is the first “Status of Fish Habitats in the United States” 

report as envisioned in the Action Plan. It summarizes the results of 

the first detailed national assessment undertaken by scientists working 

to synthesize information on aquatic habitat at a scale and level of detail 

never before attempted. This report focuses on the freshwater and estuarine 

aquatic habitats of the 50 states, which are divided into fourteen sub-regions 

for discussion. Time and resources did not permit a quantitative assessment 

of lakes, reservoirs, the Great Lakes, and marine areas, but existing information for those areas is summarized in this report. Future reports will include 

habitats not addressed in this report as well as those in U.S. territories. 

The results of the assessment are characterized as “risk of current habitat degradation,” i.e., for any particular area the data suggest some level of risk (high, 

low, or in between) that the habitat is currently in a degraded condition. The 

assessment uses “risk” of habitat degradation instead of known habitat degradation because habitat condition has not been objectively or consistently 

measured for a majority of aquatic habitats in the United States. As a result, 

the assessments for this report focus on identifying factors that are responsible 

for degrading habitat, rather than using direct measurements of habitat condition. For example, the rivers assessment uses a measure of the number of roads 

in the watershed, which is correlated with increased sedimentation and pollution, as opposed to actual measures of turbidity or heavy metals in the rivers. 

Thus the assessment can conclude that a particular river reach is at high risk of 

being degraded in its current condition, based on it having a high number of 

road crossings.

Although a large amount of data went into the assessments, some key information is missing due to the lack of nationally consistent data. Examples 

of missing information include historical and regional degradation due to 

logging, mining, or animal farming, the effect of water pumped or otherwise 

diverted from streams, and dams less than six feet high that fragment streams 

and obstruct fish passage. Because this information is missing, areas mapped 

as having a low risk of current habitat degradation due to the factors assessed 

may be under the influence of factors not included in the assessment, and thus 

actually may be at a higher risk of current habitat degradation than depicted on 

the maps. 

For the reasons explained above, readers should interpret the maps carefully.

The maps should not be understood as depicting absolute habitat condition. 

They do serve as a guide to the relative magnitude and geographic distribution 

of many factors that contribute to aquatic habitat degradation. Future reports, 

planned for 5-year intervals, will more accurately describe the condition of 

aquatic habitats, as data sources become more consistent and comprehensive. 

How to Read and 

Understand This Report

4
and fish habitat could not be incorporated into the analysis due to data limitations. These include historical land use pressures, ground and surface water 

extraction, animal feed lots, forestry practices, and regional habitat stresses 

(e.g., oil drilling), all of which will be addressed in future revisions of this 

assessment. Disturbance scores in streams affected by unmeasured factors may 

underestimate the true amount of disturbance.

The following disturbance variables were analyzed as part of the river 

assessments:

Urban/Human settlement (percent urban land use; human population 

density; road density)

Livestock and grazing (percent pasture and hay in the watershed)

Agriculture (percent row crop agriculture in the watershed)

Point source pollution data (numbers of National Pollution Discharge 

Elimination Sites, Toxic Release Inventory sites, and National 

Superfund sites); 

Habitat fragmentation (numbers of dams and road crossings) and 

Mine density.

It is important to recognize that these broadly defined disturbance variables 

may act together with other measured or unmeasured threats to degrade 

habitat. Thus, while we may identify “urbanization” as a major threat to 

some regions, “urbanization” represents an umbrella term that describes the 

many facets of urban development that cause degradation to habitats, such as 

pavement, nutrient runoff from lawns, road salt, trash and detergents getting 

into the river, etc. Rarely does only one disturbance type act alone.

Methodology for Rivers Assessment—Alaska and Hawaii

Data on human disturbances, fish populations, and habitat condition were 

limited in Alaska and Hawaii, so a simplified variation of the basic methodology used for rivers was employed for these two states. Disturbance variables 

were assigned to categories (e.g., land cover, point source pollution, infrastructure, barriers to fish movement, and industrial activity), and then a single 

5

The assessment methodologies are summarized below. Additional, more 

detailed information about the assessments can be found at the end of the 

report, and interested readers should look for the assessment methods and 

results in future peer-reviewed literature.

Methodology for Rivers Assessment—Lower 48 States

For rivers in the lower 48 states, habitat condition was estimated by analyzing 

how strongly a range of human disturbances to habitat affects river fish in all 

parts of the country, using the logic that fish reflect the quality of the habitat 

where they live. For each disturbance type, we identified the disturbance level 

at which fish with a strong reliance on high quality habitats showed marked 

declines in abundance, and where these fish disappeared from the ecosystem 

altogether. This information was used to score streams according to their most 

likely condition given the values of disturbances in each location. In the maps, 

streams that are expected to be in good condition have a low or very low risk 

of current habitat degradation, and streams in poor condition have a high risk 

of current habitat degradation. The national datasets used for this assessment 

included information about the amount of urban, agriculture, and pasture 

lands in watersheds, major point-sources of water pollution, frequency of dams 

and road crossings, and the locations of mines. Some important threats to fish 
6

score was calculated using a statistical approach called Principal Components 

Analysis. Because this methodology differs from the methodology used for the 

lower 48 states, the results cannot be directly compared—i.e., an area at high 

risk of current habitat degradation in the 48 conterminous states is not equivalent to an area at high risk of current habitat degradation in Alaska or Hawaii.

Methodology for Estuary Assessment—Lower 48 States

For the estuaries in the lower 48 states, the risk of current habitat degradation 

in each estuary was assessed by mapping national datasets of disturbance variables measured within estuaries and their adjacent watersheds. Disturbance 

variables were summarized into the following four disturbance categories:

River discharge. 

Pollution.

Eutrophication (excessive plant and algal growth as a result of increased 

nutrient input, often resulting in the depletion of dissolved oxygen). 

Current land cover and land cover change.

A relative disturbance index was assigned to each estuary for the four categories. 

The four indices were then combined to calculate a disturbance score for each 

estuary, which is a measure of the current risk of degradation to that habitat. 

Some important threats to fish and their habitat could not be incorporated 

in this analysis due to data limitations. These include, but are not limited 

to, benthic habitat loss and disturbance due to dredging and fishing practices, 

percentage of shoreline armoring, sedimentation and erosion trends, contaminant concentrations in fish and shellfish tissue, and status of biogenic habitats 

(e.g. oysters reefs and shellfish beds, coral reefs, kelp forests, and seagrass beds). 

These additional sources of disturbance will be addressed in future revisions of 

the coastal assessment. 

Methodology for Estuary Assessment—Southeast Alaska

The coastal areas of Alaska have not been mapped at the same level of detail 

as in the rest of the United States, so the assessment of estuaries in Alaska 

required that the estuaries first be delineated and entered into a Geographic 

Information System (GIS). Only the estuaries of southeast Alaska are included 

in this first assessment, but future assessments will include more coastal areas 

of Alaska. Data limitations restricted the analysis of southeast Alaska estuarine 

areas to three disturbance categories as compared to the four that were used in 

the lower 48 states: land cover, water quality/sediment toxicity, and river flow 

alteration. Data limitations also prevented the use of Principal Components 

Analysis for the last two indices; a simple percentile ranking was used instead. 

A single combined score for each estuary was calculated as the average of the 

indices. As with the river assessment for Alaska, the results of the 

southeast Alaska estuary assessment cannot be directly compared 

to the results of the estuary assessment for the lower 48 states—e.g., 

an estuary at high risk of current 

habitat degradation in the midAtlantic states is not equivalent to 

an area at high risk in southeast 

Alaska.
Lisa Wedding, NOAA CCMA Biogeography Branch

7

National Overview

Did You Know?

The United States has 181,000 square 

miles of aquatic habitat, an area 

larger than the state of California (not 

counting marine waters beyond state 

boundaries).

The United States is home to 308 

endemic fish species (i.e., fish found 

nowhere else in the world).

The southeastern United States alone 

has 1,800 aquatic species: fish, 

mussels, snails, turtles, amphibians, 

and crayfish. More than 500 of these 

1,800 aquatic species are found only in 

the southeast.

The United States is home to a diverse array 

of freshwater and marine fish, shellfish, and 

other aquatic species. More than 3,000 

species of fish inhabit America’s streams, rivers, 

lakes, reservoirs, marshes, swamps, bays, estuaries, 

coral reefs, seagrass beds, shallow water banks, 

deep ocean canyons, and other watery habitats. 

The United States is also home to more than 300 

million people, all depending to some extent on the 

same water that fish call home. Agriculture, urbanization, and other effects of human inhabitation 

occur over most of the U.S. landscape, altering to 

varying degrees water flow, water quality, and many 

other characteristics of aquatic habitat. Few aquatic 

habitats in America are unaffected by human 

activity; some have been severely degraded, and 

some less so. The map below depicts the results of 

the habitat assessments conducted for this report, 

with the estuarine areas offset for better visibility.

0 500250

km

0 100 200

km
8

Overall, 27 percent of the miles of stream in the 

lower 48 states are at high or very high risk of 

current habitat degradation, and 44 percent are at 

low or very low risk. In the United States, areas of 

high risk and low risk of current habitat degradation occur in discernable patterns. 

Habitats with a very high risk of current habitat 

degradation include those in or near urban development, livestock grazing, agriculture, point source 

pollution, or areas with high numbers of active 

mines and dams. Specific locations that stand out 

as regions at high risk of current habitat degradation include: the urban corridor between Boston, 

and Atlanta, the Central Midwestern states of Iowa, 

Illinois, Indiana, and Ohio; the Mississippi River 

Basin, including habitats adjacent to the lower 

Mississippi River in Arkansas, Mississippi, and 

Louisiana; habitats in eastern Texas; and habitats in 

central California and along the Columbia River in 

Oregon and Washington. 

Areas that stand out as being at very low risk 

according to the parameters in this report include 

rural areas in New England and the Great Lakes 

states; many habitats throughout the Mountain, 

Southwest, and Pacific Coast States; as well as most 

of Alaska. It should be noted that not all water 

and land management issues could be addressed 

in the assessment, so some of the areas mapped as 

at low risk of current habitat degradation actually 

may be at higher risk due to disturbance factors 

not assessed. For example, most arid regions of 

the western United States were found to be at low 

risk of current habitat degradation. Water quantity 

is a critical limiting factor for 179 species of desert 

fishes, yet stream flow and water extractions were 

not accounted for in the assessment. The maps 

likely overestimate the amount of habitat at low 

risk of current habitat degradation in the arid west.

The estuaries of the lower 48 states show patterns 

similar to those of the land areas, which is not 

surprising because most of the disturbances to estuarine habitats originate on land. Estuaries in the 

mid-Atlantic have a very high risk of habitat degradation related to polluted run-off and other effects 

of the intense urbanization and agriculture in this 

area. The estuaries of southern California also have 

a high risk of current habitat degradation for similar 

reasons. Estuaries in the north Pacific and Downeast 

Maine have a low risk of current habitat degradation. Overall, 23 percent of the estuaries (by area) 

in the lower 48 states are at low or very low risk 

of current habitat degradation and 53 percent are 

at high or very high risk of current habitat degradation. Marine habitats of the United States tend 

to be most degraded near the coast, where they are 

most affected by human activity.

Lower 48 states — Risk of Current Degradation

15%

24%

25%

8%

28%

Very Low

Low

Moderate

High

Very High

% Estuary Area

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40

% Stream Length

9%

18%

29%

38%

6%

Lower 48 states — Risk of Current Degradation
Did You Know?

The Northeastern states have the second 

largest value of commercial catch (after 

Alaska), with more than $830 million 

of catch in 2009. In addition, marine 

and freshwater recreational fishermen 

spent more than $2.5 billion on fishing 

expenditures in these states in 2006. 

More than half of the original wetlands in 

the northeastern states have been filled 

or converted to agricultural lands.

Atlantic salmon were once native to 

almost every U.S. river north of the 

Hudson River; remnant wild populations 

are now known in only 11 rivers. 

Fish Habitat in the Northeastern States

S

everal centuries of development activities throughout the northeast have resulted 

in extensive alteration and loss of aquatic 

habitats in some areas. In general, northern areas are 

at lower risk of current degradation than southern 

areas, where population pressures are most intense. 

The primary sources of current habitat degradation 

in eastern Massachusetts and central Connecticut 

are urbanization, road crossings, and pollution. 

Row crop agriculture and pasture are responsible 

for the high risk of current habitat degradation in 

western New York. Overall, almost 60 percent of 

the miles of streams in the northeastern states have 

a low or very low risk of habitat degradation; only 

16 percent have high or very high risk. In contrast, 

44 percent of the estuarine area is at high or very 

high risk of current habitat degradation, including 

Massachusetts Bay, Narragansett Bay, and Long 

Island Sound. 

Robert Michelson, Used under license agreement with USFWS

9

Northeastern States

(Maine, New Hampshire, Vermont, New York, Massachusetts, Rhode Island, Connecticut)

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation
Human Activities Affecting Fish Habitat

Urban land use 

The northeast is one of the most urbanized areas in 

the country, with a high percentage of impervious 

surfaces in some of its watersheds. These impervious surfaces alter the hydrology of streams and 

increase sedimentation in rivers, lakes, and bays. 

Another effect of urbanization is loss of habitat as 

wetlands are filled, streams diverted, and channels 

dredged.

Point source pollution

The northeast once supported numerous industries 

that discharged contaminants such as heavy metals 

and PCBs into the region’s waters. The number 

of industrial sites is much lower today, but their 

legacy—as pollution leaks from abandoned industrial sites or disposal areas—often remains. Over 

time, these contaminants concentrate in sediments 

at the bottom of rivers, lakes, and bays. Some of 

the highest concentrations in the northeast occur 

in Narragansett Bay, New York/New Jersey Harbor 

and Bight, and western Long Island Sound, where 

elevated levels of metals (e.g., arsenic, chromium, 

mercury, nickel, silver, and zinc), PCBs, and pesticides occur. Contaminants often find their way 

into the food chain, affecting fish directly by killing 

them or indirectly by affecting growth, behavior, 

and reproduction, and sometimes making them 

unsuitable for human consumption. Almost onethird of fish tissue specimens collected by the Environmental Protection Agency (EPA) in northeast 

coastal areas contained concentrations of contaminants above levels recommended for human 

consumption, reducing our nation’s potential 

seafood supply. 

Robert Michelson, Used under license agreement with USFWS

Fish with Habitat Trouble

Fish that migrate between the ocean and 

freshwater streams—such as American 

shad, Atlantic salmon, blueback herring, 

alewife, American eel, Atlantic sturgeon, 

and shortnose sturgeon—have declined 

as a result of culverts, weirs, dams, 

and other human-made barriers to their 

migration.

Lake chub, lake sturgeon, and other 

lake fish have declined as a result of 

urbanization, barriers to migration and 

increased sedimentation in lakes.

American brook lamprey, channel darter, 

eastern sand darter, and stonecat have 

declined as a result of loss of clean 

stream gravel and rock in spawning 

habitats from excessive sediment inputs.

Atlantic salmon

10

Northeastern States — Risk of Current Degradation

28%

13%

35% 15%

9%

Very Low

Low

Moderate

High

Very High

% Estuary Area

Northeastern — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50 55

% Stream Length

2%

14%

25%

50%

9%
Dams and other barriers

The northeastern states contain thousands of 

dams, most built before 1910 for agricultural and 

industrial uses, and a few built more recently for 

flood control, recreation, water supply, and energy 

generation. In many cases, the dams have outlived 

their industrial usefulness, but continue to block 

the passage of migratory fish species to and from 

their historic upstream spawning grounds. Poorly 

constructed culverts and other types of road crossings also have negative effects on fish migration, 

tidal exchange, and stream flow, which directly 

affect fish growth and reproduction.

Proposed renewable ocean energy projects

Numerous uncertainties are associated with the 

potential effects of forthcoming renewable ocean 

energy projects (such as ocean-based wind power 

and ocean current power) on coastal and marine 

habitats. Only time, careful evaluation, and monitoring will reveal the effects of these technologies.

Working for Change

The Machias River, Maine 

The Machias River system in “downeast” Maine is 

important habitat for Atlantic salmon and eastern 

brook trout. With 86 percent of the Atlantic 

salmon habitat within the Machias River system 

under permanent protection, restoration efforts 

have moved to its major headwater tributaries, 

including the West Branch of the Machias River. 

As part of an effort by the Eastern Brook Trout Joint 

Venture and “Project SHARE,” by the end of 2010 

all but two of the single road-stream crossings in 

the West Branch Machias River sub-watershed will 

be fitted with open-bottom arched culverts that 

are designed to allow fish to pass and provide for 

a natural stream channel. This project is a small 

part of a larger conservation strategy developed by 

the Eastern Brook Trout Joint Venture to address the 

current threats to this species.

Katrina Mueller, Project SHARE

Katrina Mueller, Project SHARE, Machias River

11
12

Did You Know?

The Mid-Atlantic states’ marine and 

freshwater recreational fishing expenditures 

were greater than $3.7 billion in 2006, and 

the values of commercial fish catch totaled 

just less than $375 million in 2009.

The main stem of the Delaware River is 

the longest undammed river east of the 

Mississippi, providing unobstructed 

migratory fish habitat for 330 miles.

The Chesapeake Bay contains zones of 

low oxygen, the result of pollution from 

the surrounding watershed, that threaten 

crab and other important fish populations 

in the bay.

Fish Habitat in the Mid-Atlantic States

The headwater streams of West Virginia, 

Virginia, Maryland, and Pennsylvania have 

a low risk of current habitat degradation 

due to the factors assessed, particularly in central 

West Virginia and northwest Pennsylvania. Many 

of these streams, however, are degraded by excess 

acidity and sediments that result from current and 

legacy mining activities, which have not been fully 

analyzed in this assessment. In southeast Pennsylvania, row crops and pasture are responsible for 

areas with a very high risk of current habitat degradation. 

Mid-Atlantic States

(Pennsylvania, New Jersey, West Virginia, Virginia, Maryland, Delaware) Jane Thomas IAN Image Library (ian.umces.edu/imagelibrary/)

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation
Fish with Habitat Trouble

Brook trout populations have been 

eliminated from 25 to 35 percent of 

the watersheds in this region because 

of acid mine drainage, increased water 

temperature, and sedimentation. 

Populations of Atlantic menhaden, an 

important forage fish in estuarine and 

marine food webs, have declined 85 

percent in the past 30 years, possibly 

due to human-induced changes in the 

ocean and coastal bays combined with 

the effects of overfishing.

Shad and river herring—important as 

forage, recreational, and commercial 

fish—have experienced substantial drops 

in population due to dams, poor water 

quality, and overharvesting. 

13

Along the developed corridor that stretches from 

northeast New Jersey through central Maryland and 

northwest Virginia, urbanization is a major factor in 

areas with a very high risk of current habitat degradation. Intensive pasture and road crossings are the 

major concerns on the Delmarva Peninsula. Reservoirs in the mid-Atlantic states have been degraded 

by nutrient enrichment and sedimentation. Many 

rivers in the mid-Atlantic have significant barriers to 

fish movement. These barriers are related to large 

reductions in the numbers of spawning American 

shad, blueback herring, American eels, and Atlantic 

sturgeon. Overall, the greatest proportion of the 

rivers in the mid-Atlantic falls into the moderate 

category of risk of habitat degradation from the 

factors assessed, with slightly less than one-third 

falling into the low risk category.

The mid-Atlantic states contain the largest estuary in 

the continental United States, the Chesapeake Bay, 

which has a very high risk of current habitat degradation because its surrounding watershed is highly 

altered by disrupted water flows as well as urbanization and agriculture, which contribute excess 

nutrients and sediments to the estuary. Ninety-five 

percent of the estuarine area in the mid-Atlantic 

states is at high or very high risk of current habitat 

degradation and these estuaries have some of the 

worst pollution scores of all the estuaries assessed.

Human Activities Affecting Fish Habitat

Urban land use and pollution

Runoff and other land-based pollution from large 

riverside cities such as Philadelphia, Pittsburgh, 

Wilmington, and Washington, DC, adversely affect 

fish habitats in the Delaware, Susquehanna, Ohio, 

and Potomac rivers. Surrounding these large cities 

are smaller cities and suburban areas that create a 

concentration of human population and impervious surfaces extending from New Jersey through 

southeastern Pennsylvania, Delaware, central 

Maryland, and southeastern Virginia to the coastal 

areas of the Mid-Atlantic, including the Delaware 

and Chesapeake bays. Runoff from urban and 

suburban areas typically contains many pollutants 

Mid-Atlantic — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40

% Stream Length

7%

22%

37%

32%

1%

Mid-Atlantic — Risk of Current Degradation

23%

72%

5%

Very Low

Low

Moderate

High

Very High

% Estuary Area

hickory shad
14

such as motor oil, heavy metals, pesticides, and 

sediments. Elevated levels of metals (e.g., arsenic, 

chromium, mercury, nickel, silver, and zinc), PCBs, 

and DDT are found in the sediments of the upper 

Chesapeake Bay and Potomac River.

Mining and other resource extraction

Drainage from coal mines and coal refuse piles is a 

common problem in the Appalachian coal region. 

In 2010, 5,475 linear miles of streams in Pennsylvania did not meet EPA-mandated in-stream water 

quality standards due to more than a century of 

mining. Coal mine drainage releases acid into 

streams, making them thousands of times more 

acidic than unaffected streams and eliminating a 

majority of native aquatic species. For example, 

in West Virginia, the practice of “mountaintop 

removal” mining has resulted in the burial of many 

headwater streams and elevated concentrations of 

selenium, a toxic element, in downstream waters. 

Pennsylvania, West Virginia, and New York are also 

threatened by current and proposed hydrofracture 

drilling for natural gas, which can release pollutants into aquatic areas.

Dams and other barriers

There are over 5,000 dams in the mid-Atlantic states. 

The great majority of these dams are small (i.e., less 

than 15 feet high) and many of these small dams 

are obsolete and in disrepair. Small dams, as well 

as many poorly designed culverts and road crossings, fragment habitat for shad and river herring, 

smelt, American eel, and other fish species that 

either migrate for spawning or require unobstructed 

access throughout waterways to complete their lifecycles. Large dams have also resulted in significant 

changes to aquatic ecosystems in the mid-Atlantic 

states. A number of dams built on the Hackensack 

River in New Jersey are responsible for the conversion of a unique native white cedar swamp into the 

8,400-acre New Jersey Meadowlands, an area now 

dominated by the common reed.

Working for Change

South Fork Little Conemaugh River, 

Pennsylvania

Past mine activities along the Conemaugh River 

have resulted in chronic acid mine drainage into 

the stream, which has increased the acidity of the 

stream and reduced the abundance of brook trout 

and other aquatic life. In addition, erosion from a 

300-foot stretch of the stream bank on the South 

Fork was greatly increasing sediment inputs to the 

river. With help from over a dozen partners, the 

Eastern Brook Trout Joint Venture is using limestone to neutralize the river’s acidity and promote 

the recovery of brook trout populations and other 

aquatic life. Another phase of the project will stabilize the stream by installing fish habitat structures 

along the stream banks where there is a significant threat of erosion. This project is a small part 

of a larger conservation strategy developed by the 

Eastern Brook Trout Joint Venture to restore brook 

trout habitat and populations.

USFWS, South Fork Little Conemaugh River
15

Did You Know?

The southeast Atlantic states’ marine 

and freshwater recreational fishing 

expenditures were greater than $3.5 

billion in 2006 and commercial fish catch 

totaled more than $108 million in 2009.

The Albemarle-Pamlico Sound in North 

Carolina is the second largest estuary in 

the United States, with a watershed of 

approximately 30,000 square miles. It 

provides nursery habitat for 90 percent 

of fish and shellfish caught by commercial 

fishermen in the region.

The human population in the Southeast 

Atlantic states is projected to grow 76 

percent by 2030 which, without careful 

planning, will further degrade fish habitat 

and reduce fish populations.

The aquatic habitats of the southeast show 

a wide range of risk of current habitat 

degradation based on the factors assessed. 

Overall, the greatest proportion of the rivers in the 

southeastern Atlantic states falls into the moderate 

category of risk of habitat degradation from the 

factors assessed, with 31 percent falling into the low 

risk category. Atlanta, Augusta, Charlotte, Raleigh/

Durham, and the suburban corridors between them 

have a very high risk of current habitat degradation related to urbanization of the surrounding 

watersheds, road crossings, and agriculture in the 

outlying areas. The mountains of North Carolina 

and most of the coastal plain of all three states 

Southeast Atlantic States (North Carolina, South Carolina, Georgia)

Fish Habitat in the Southeast Atlantic States

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation
Fish with Habitat Trouble

Annual catch of river herring in Albemarle 

Sound averaged 12 million pounds from 

1880 to 1970, but collapsed to only 

100,000 pounds in 2005. A specific 

cause of the decline has not been 

identified, but habitat loss is believed to 

be one of many contributing factors.

Southern Appalachian brook trout have 

declined sharply due to the effects of 

historical logging and the introduction 

of non-native brown and rainbow trout. 

Today they face the additional threat of 

excess sedimentation caused by human 

alterations to the landscape.

Roanoke bass and smallmouth bass are 

losing habitat as a result of sedimentation 

and human alterations to river flows. 

herring

16

have a low risk of habitat degradation, although 

development is intensifying on some of the barrier 

islands of the coast. Although many of the smaller 

estuaries in the southeast Atlantic states have low 

or very low risk of current habitat degradation, the 

largest estuary, Albemarle-Pamlico Sound, has a 

high or very high risk of current habitat degradation due to agricultural runoff containing excess 

nutrients and pollutants. Some of the estuaries 

with overall moderate risk of current habitat degradation have a very high risk of degradation from 

pollution; these include Charleston Harbor and the 

Santee River, which had some of the highest pollution risk scores in the region. 

Human Activities Affecting Fish Habitat

Urban land use

The southeastern states contain the urban centers 

of Columbia, Charlotte, Raleigh, Greensboro, 

and Atlanta. In these cities and the surrounding 

suburbs, large areas of impervious surfaces replace 

natural streamside habitat, increase pollution and 

sedimentation, and alter hydrology. Declining fish 

populations are the result, near the cities as well 

as downstream. Another effect of urbanization 

is demand for water. From 2007 through 2009, 

drought conditions in the southeast led to disputes 

over allocation of water between humans and fish.

Dams and other barriers

Over 1,000 dams impound rivers and streams in 

the southeast Atlantic states. Dams impede migrations of striped bass, American shad, and herring 

as they swim upstream from the Atlantic Ocean 

to spawn. In many cases, these blockages restrict 

access to historical spawning habitats and limit 

adequate spawning flows necessary for egg and fry 

survival. 

Agriculture

Since European settlement, the wide coastal plain 

of the southeast Atlantic states has been used for 

large agricultural operations producing tobacco, 

cotton, peanuts, corn, soybeans, and many other 

agricultural products. Increasing use of irrigation 

for these row crops has changed water flow in many 

of the region’s streams. More recently, intensive 

Southeast Atlantic — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50

% Stream Length

8%

18%

44%

31%

1%

Southeast Atlantic — Risk of Current Degradation

2%

11%

9%

5% 73%

Very Low

Low

Moderate

High

Very High

% Estuary Area
17

hog and chicken farming have become important as well. Concentrated animal operations can 

add additional stress because the waste generated 

by these operations affects streams and estuaries 

through runoff, or when waste-holding ponds fail. 

Improperly managed runoff from farms contributes excess sediments and nutrients to streams, 

which interferes with fish spawning and can lead to 

potentially harmful algal blooms. 

Working for Change

Jockey’s Ridge State Park, North Carolina

Before this area became a state park, vegetation 

was cleared in preparation for planned development in the northern part of what is now Jockey’s 

Ridge State Park. The loss of vegetation allowed 

sand from the largest active dune system on the 

U.S. East Coast to blow directly on the fringing 

salt marsh along Roanoke Sound. The marsh and 

shoreline have been further weakened by wind and 

wave erosion. The Southeast Aquatic Resources 

Partnership along with the North Carolina Coastal 

Federation and its partners are restoring the natural 

marsh within Jockey’s Ridge State Park by building 

an oyster reef sill and replanting the marsh grasses 

and riparian vegetation, establishing natural buffers 

that prevent both wind and wave erosion. To date, 

over 139 volunteers have been involved in the 

planting, which benefits fish such as snook, sheepshead, grouper, redfish, spotted sea trout, and black 

drum. This project is one of many that are planned 

to address one of the objectives of the Southeast 

Aquatic Resources Partnership Aquatic Habitat 

Plan: “Conserve, restore, and create coastal estuarine and marine habitats.” 

Friends of Jockey’s Ridge, Jockey’s Ridge State Park

Friends of Jockey’s Ridge, Jockey’s Ridge State Park
Did You Know?

The upper midwest states had the second 

greatest total expenditures for freshwater 

recreational fisheries of all the regions in 

2006. More than $6 billion were expended 

for recreational fisheries, and an additional 

$13 million was brought into the region 

through commercial catch in 2009. 

The upper midwest has 33,000 lakes—more 

than 25 percent of the nation’s lake habitat.

While lake sturgeon populations are still 

very depressed, both lake trout and lake 

whitefish fisheries have been rehabilitated 

in some lakes, supporting both sport and 

commercial fisheries. 

Fish Habitat in the Upper Midwest states

Michigan, Wisconsin, and Minnesota 

border four of the five Great Lakes 

(lakes Michigan, Superior, Huron, 

and Erie) and also contain thousands of smaller 

lakes. The Upper Mississippi River flows through 

the Upper Midwest states, from its headwaters in 

Minnesota along the boundary between Minnesota and Wisconsin. A unique region of deeply 

carved river valleys known as “The Driftless Area” 

is located in southwestern Wisconsin and southeastern Minnesota. 

Lakes and reservoirs in the upper midwest states 

have seen monumental changes in water quality 

and fish assemblages over the past 200 years. AgriVery low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

18

Upper Midwest States (Minnesota, Wisconsin, Michigan) Pat Rivers
culture, logging, overharvesting of fish, manufacturing, urban and suburban development, construction of thousands of dams (many abandoned), and 

the introduction (both accidental and intended) of 

non-native species have degraded habitat, collapsed 

food webs, and threatened fish populations and 

human health. Fortunately, bi-national efforts have 

resulted in improvements in water quality in all of 

the Great Lakes, but much remains to be done as 

urbanization, legacy industrial wastes, and agriculture continue to affect the Great Lakes and the 

smaller glacial lakes of the region. 

Similarly, agricultural runoff and excess sediment 

threaten upper Mississippi River aquatic resources. 

The areas with the lowest risk of habitat degradation occur in the northern parts of the region, 

which have mostly recovered from historical effects 

of logging and mining. The areas with the highest 

risk of degradation occur in southwest Minnesota, 

where row crops dominate the landscape, and in 

the urban areas around Detroit, Milwaukee, and 

Minneapolis. Overall, the greatest proportion of 

the rivers in the upper Midwest states falls into the 

Fish with Habitat Trouble

Fish that migrate from the Great Lakes to 

rivers, like lake sturgeon, have declined 

because of dams and other barriers. 

In many areas, non-native zebra and 

quagga mussels have altered food webs 

for native fish and negatively affected 

native mussel populations.

Fish that use native vegetation for 

spawning and nurseries such as 

northern pike, yellow perch, walleye, and 

muskellunge (“muskies”), lose habitat 

when lakefront property owners remove 

aquatic “weeds”

moderate category of risk of habitat degradation 

from the factors assessed, with 27 percent and 25 

percent falling into the low risk and high risk categories, respectively.

Human Activities Affecting Fish 

Habitat

Urban land use

Major cities such as Detroit, Milwaukee, Minneapolis/St. Paul, and numerous smaller lake-front cities 

support a population of about 35 million people 

in the upper midwest area. The resulting urbanization has reduced fish habitat through wetland fill 

and the conversion of natural lake shorelines to 

bulkheads and seawalls. In smaller lakes, vacation 

communities with multiple tiers of development 

threaten lake and reservoir habitat through habitat 

loss and the input of excessive nutrients and 

sediments.

19

Upper Midwest — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50

% Stream Length

4%

25%

42%

27%

2%

Harry and Laura Nohr Chapter of Trout Unlimited

northern pike
Point source pollution

A major hub for manufacturing and transportation, 

the Great Lakes were once a dump site for many 

toxins, including mercury, PCBs, and dioxins. As 

a result of the Clean Water Act most of these direct 

pollution discharges have stopped, but the pollutants remain because many are trapped in lake and 

stream sediments. Other pollutants that stay in the 

water have long residence times because less than 1 

percent of the water in the Great Lakes exits the lake 

system annually. Discharge from sewage treatment 

systems remains a problem, particularly where 

stormwater and sewage systems are combined in 

large urbanized areas.

Dams and other barriers

Dams and other barriers are having a significant 

effect on fish habitat in the upper Midwest. For, 

example, in the Lake Michigan watershed alone, 

dams, culverts, and road crossings that impede 

fish migration have reduced nearly 19,000 miles of 

available stream habitat to only 3,300 miles. With 

an estimated one-third of all Great Lakes fish using 

tributaries as their principal spawning and nursery 

habitats, these barriers are a significant factor in the 

decline of fish populations in the Great Lakes and 

other waters with similar barriers.

Agriculture

Corn and other row crops dominate the landscape across southern Minnesota, Wisconsin, and 

Michigan. Most of this agricultural activity came 

at the expense of the large wetland complexes that 

were found across the landscape in this region. The 

region has been extensively tile drained and streams 

turned into drainage ditches, devoid of fish habitat. 

Eroded soil and fertilizer run off the land surface 

into lakes and rivers, reducing water clarity, stimulating algal growth, and changing the bottoms of 

river channels and lakes from sandy sediments to 

mud.

Working for change

Cass County, Minnesota

Cass County’s 500-plus high-quality lakes provide 

critical fish and wildlife habitat, are the basis for 

many Minnesotans’ recreational enjoyment, and are 

key to sustaining local communities. While some 

areas of the region lost population in recent years, 

lake-rich counties like Cass are seeing dramatic 

increases both in year-round and seasonal residents. Projections for future growth and development of lakeshores show this trend will continue. 

Cass County’s 55 most developed lakes still have 

approximately 38 percent of the shore undeveloped 

or minimally developed. A number of these lakes 

have been surveyed by the Minnesota Department 

of Natural Resources’ (DNR) Sensitive Lakeshore 

Identification Pilot Project. A partnership between 

Cass County, the Leech Lake Area Watershed Foundation, the Minnesota Department of Natural 

Resources, and the Midwest Glacial Lakes Partnership seeks to secure voluntarily donated conservation easements from willing landowners on 12 to 

15 of the most vulnerable shoreland properties in 

the county. As a result, approximately 1,200 feet of 

shoreline and its fish and wildlife habitats will be 

protected, and continued recreational enjoyment 

and economic stability will be ensured.

Pat Rivers

20
Did You Know?

Greater than $2.7 billion in expenditures 

were associated with recreational fishing in 

the central midwest states in 2006.

The Ohio River drainage provides habitat 

for at least 350 species of fish and more 

than 120 mussel species—almost half of 

the freshwater fish and over one-third of all 

mussel species found in the United States.

There are 30,700 miles of streams and 

rivers in the upper Mississippi River basin, 

a landscape of 189,000 square miles, 

two-thirds of which supports agriculture. 

The central midwest states include parts 

of the major watersheds of the Ohio and 

Illinois Rivers and part of the Upper Mississippi River watershed. These states also border 

lakes Michigan and Erie, and contain numerous 

reservoirs and smaller lakes.

The central midwest states have experienced a long 

history of manufacturing, agriculture, and mineral 

extraction. As a result, substantial areas (40 percent 

of the miles of rivers assessed) have a high risk of 

habitat degradation due to the factors assessed, 

particularly in Iowa and the northern parts of 

Illinois, Indiana, and Ohio. Row crops and pasture 

are the most common factors contributing to the 

risk of habitat degradation in these areas. Areas 

Fish Habitat in the Central Midwest states

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

21

Central Midwest States

(Iowa, Illinois, Indiana, Ohio)

Chris Barnhart
Robert Michelson, used under license agreement with USFWS

with a low risk of habitat degradation occur in the 

southern parts of the region. Overall, the greatest 

proportion of the rivers in the central midwest 

states falls into the moderate category of risk of 

habitat degradation from the factors assessed.

Human Activities Affecting Fish 

Habitat

Urban land use

In the 1990s, urban land in Ohio, Illinois, and 

Indiana increased by about 10 percent. Currently, 

Ohio and Illinois are among the 10 most populous 

states in the nation, with Indiana and Iowa in the 

top 20. Large cities such as Chicago, Indianapolis, Columbus, and Cleveland have created large 

areas of impervious surfaces and a great amount 

of urban pollution near the rivers and lakes of this 

area, degrading fish habitat through changes in 

hydrology and excessive inputs of nutrients and 

sediment.

Point source pollution

Northern Ohio, Indiana and Illinois are part of the 

Factory Belt, an area that was a primary center of 

manufacturing and industry in the late 1800s and 

early 1900s. Many of the manufacturing processes 

resulted in discharges of toxins to locals waterways. PCBs and dioxins, which have been banned 

for more than a decade, still pose a problem in the 

area’s rivers, lakes, and reservoirs because these 

industrial chemicals do not break down over time.

Agriculture

Ohio, Indiana, Illinois, and Iowa constitute the 

majority of what is known as the Corn Belt, the 

most intensive agricultural region in the midwest 

where corn and soybeans are the predominant 

crops. Most of the corn and soybean is fed to livestock, making this a key area for the production 

of hogs, chickens, and cattle. Runoff and drainage 

from agricultural fields and feed lots, and from 

Central Midwest — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50 55

% Stream Length

6%

40%

47%

7%

0%

Fish with Habitat Trouble

Lake sturgeon and shovelnose sturgeon 

have declined steadily since lock and dam 

systems were built on the major rivers of 

this region. Lack of access to spawning 

areas, as well as loss of their preferred 

food (mussels and snails) due to habitat 

degradation, are thought to be responsible 

for their decline.

Native brook trout populations have declined 

because of landscape changes that affected 

stream hydrology and temperature and the 

loss of shaded streamside habitat.

The pugnose minnow was historically 

abundant in the central midwest states 

where clear water with aquatic vegetation 

was present. Due to this kind of habitat 

becoming increasingly rare, this species 

is on the verge of being extirpated from 

the region.

22

brook trout 
23

stream banks eroded by cattle, have resulted in 

elevated levels of nitrogen, phosphorus, and sediments in most of the streams in the area.

Working for Change

Little Turkey River, Northeast Iowa

The Little Turkey River is a popular trout stream in 

the Turkey River watershed of northeast Iowa. It 

was identified by the Iowa Department of Natural 

resources as a top-priority stream in need of 

water quality and habitat improvements because 

degraded habitat in the upper 2-mile coldwater 

portion of the stream limits natural reproduction 

of trout. Willing landowners in the upper part of 

the watershed have installed conservation terraces, 

grassed waterways, erosion control structures, and 

other habitat improvements in an effort to reduce 

soil loss and improve habitat quality for fish and 

wildlife. In 2008–2009, about a mile of actively 

eroding stream bank was resloped and stabilized, 

and riparian areas were seeded with native vegetation. The coordination of upland, riparian, and 

in-channel enhancement efforts on this stream 

have improved habitat for brook and brown trout, 

longnose dace, fantail darter, and other fish species. 

This project is but one of many that will be undertaken by the Driftless Area Restoration Effort as they 

implement their mission of “Working together to 

protect, restore and enhance cold, cool, and warmwater streams for fish and other aquatic life in the 

Driftless Area region for future generations.”

USFWS, Little Turkey River, pre-restoration

USFWS, Little Turkey River, post-restoration
Did You Know?

Recreational fishing expenditures in the 

central Mississippi states totaled more than 

$2.9 billion in 2006, with a majority coming 

from recreational fishing 

in Missouri.

In Tennessee’s Duck River there are more 

fish species per mile than in any other river 

in North America. 

Hydroelectric development in Arkansas’ 

White River has changed the water 

temperature in portions of the river. Once 

a coolwater smallmouth bass stream, it 

is now a cold-water system that supports 

introduced rainbow and brown trout 

fisheries.

The Central Mississippi River states contain 

the confluences of the Mississippi River 

with the Ohio, Missouri, and Arkansas 

rivers. Alteration of these large rivers for transportation and flood control has substantially altered 

their ecological characteristics, eliminating natural 

floodplains, sandbars, and meanders, and impeding 

fish migration routes. Other major rivers include 

the Tennessee, Cumberland, Kentucky, and Osage. 

Reservoirs on these and other rivers have increased 

recreational fishing in the area, but are suffering 

from the highest rates of oxygen deprivation of 

reservoirs in the country. 

Fish Habitat in the Central Mississippi River states

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

24

Central Mississippi River States (Missouri, Arkansas, Kentucky, Tennessee) Stan Allen
David Ostendorf, Missouri Department of Conservation

Aquatic habitat close to the Mississippi River has a 

very high risk of degradation from row crop agriculture. Areas with a high risk of habitat degradation also occur in southwest Missouri and central 

Kentucky and Tennessee, where pasture is the 

primary factor contributing to habitat. All four 

states contain areas with a lower risk of habitat 

degradation, particularly western Arkansas and 

eastern Kentucky. Overall, 40 percent of the rivers 

in the Mississippi River states have a high or very 

high risk of current habitat degradation from the 

factors assessed, with 34 percent falling into the 

moderate category.

Human Activities Affecting 

Fish Habitat: 

Agriculture 

Kentucky, Tennessee, and Missouri rank in the top 

five states for number of farms. Cattle and poultry 

are the most common livestock, and tobacco, 

cotton, corn, soybeans, and rice are among the 

most frequently grown crops. Streams degraded 

by agriculture are most common in the “boot 

heel” (southeast) of Missouri and eastern Arkansas. 

Stormwater runoff from agricultural fields carries 

sediment, fertilizers, and pesticides into the Mississippi River and its tributaries. Atrazine, a herbicide used on corn and soybeans, is ubiquitous in 

this area. The most ecologically significant effect 

of the agricultural runoff into the Mississippi River 

is the “dead zone” created in the Gulf of Mexico 

each summer where excess nutrients stimulate algal 

growth, which in turn depletes available oxygen 

concentrations in the water.

Point source pollution

Regional industries have contributed significant 

amounts of oil, aluminum, lead, and other industrial wastes such as sulfur dioxide, hydrogen sulfide, 

and benzene to the flow of the Mississippi. Many 

chemicals, such as PCBs, have been banned for 

decades but persist in the river’s suspended and 

bottom sediments. Poorly treated sewage and 

wastewater is also a concern because it contributes 

bacteria and detergents to the river water. 

Central Mississippi — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40

% Stream Length

13%

27%

34%

25%

0%

Fish with Habitat Trouble

Many darters (and logperch) are under 

threat of extinction due to mining, 

logging, industrial development, and 

residential development, which increase 

sedimentation in the fast, clear streams 

inhabited by darters.

Pallid sturgeon and shovelnose sturgeon, 

once common in the Mississippi 

River, have declined in part from river 

modifications for navigation.

25

Missouri saddled darter
Working for 

Change

Little Borbeuse 

Creek, Meramec 

River Basin, 

Missouri

Rural landowners along 

the Little Borbeuse 

Creek in Missouri are 

working together to 

protect their livelihood 

and fish habitats in 

the Meramec River Basin. With the assistance of the State 

Department of Conservation and Department of Natural 

Resources, landowners formed a committee to put conservation decision-making in the hands of the landowners. 

Through tours of farms currently implementing conservation measures, such as off-stream watering practices to 

improve stream turbidity and decrease soil erosion, other 

farmers were able to learn about the materials and techniques needed to replicate the projects on their land. 

Further, local contractors and landowners benefited from 

cooperation, saving both time and money by completing 

multiple projects at once. The Little Borbeuse Creek landowner committee was the first project funded with National 

Fish Habitat Action Plan Funds after its nomination by the 

Fishers and Farmers Partnership, showing the importance 

of conservation partnership to the National Fish Habitat 

Action Plan. This project illustrates how cooperation 

between farmers and state conservation professionals can 

lead to improved stream quality and fish habitat.

26

David Ostendorf, Missouri Department of Conservation, Meramec River
27

Focus on the Gulf of Mexico

This report includes a focus on the Gulf of 

Mexico, in recognition of the interest in 

this area generated by the catastrophic 

Deepwater Horizon oil spill in April 2010. Much 

is still unknown about the effects of the oil spill, 

so this report does not assess the effects of the oil 

spill but instead provides a description of baseline 

conditions against which to gauge future habitat 

assessments. In the wake of the oil spill, commercial and recreational fishery closures affected up to 

one-third of Gulf of Mexico federal waters. The oil 

visibly affected thousands of birds, fish, and other 

wildlife, and the extent of the damage beneath the 

water is unknown at this time. Despite these uncertainties, one thing is clear: never has the importance 

of healthy fish habitat been more evident. From 

the fishermen and beachgoers along the Gulf to the 

President of the United States, there is agreement 

on the need for continued and deliberate protection and restoration of these aquatic habitats. 

Fish Habitats in the Gulf of Mexico 

Coastal and marine habitats of the Gulf of Mexico 

include submerged aquatic vegetation, mangrove 

wetlands, mud flats, oyster reefs, estuarine emergent 

marsh, hard bottom, corals, and water column. 

Collectively, these diverse coastal and marine 

habitats provide spawning, nursery, feeding, and 

shelter habitat for a myriad of recreationally and 

commercially important fish and invertebrate 

species in the Gulf of Mexico. The most productive 

estuarine areas include the Apalachicola, Mobile, 

Tampa, and Galveston bays, the Suwannee, 

Atchafalaya, and Mississippi rivers and their 

associated wetlands. 

Fisheries and tourism industries throughout 

the Gulf of Mexico depend on healthy aquatic 

habitats. Tourism is the second largest industry 

in the Gulf, behind oil. About 46 percent of the 

Gulf economy, or over $100 billion a year, comes 

from tourism dollars. The Gulf of Mexico also 

is extremely important to both commercial and 

recreational fishing. Ports in the Gulf of Mexico 

states, including Florida’s Gulf Coast, took in more 

than $525 million worth of commercial fish and 

Guy Fanguy

NOAA
28

shellfish in 2009, 13.5 percent 

of total national catch value. 

Approximately 73 percent of 

total U.S. shrimp landings 

occurred in the Gulf of Mexico 

region and 30 percent of total 

U.S. marine recreational fishing 

trips were taken in the Gulf of 

Mexico in 2008.

Human Activities Affecting 

Fish Habitat

Oil and gas exploration

With over 4,000 active oil and gas platforms, the 

Gulf of Mexico is one of the most important regions 

for oil and gas production in the United States. 

Offshore oil production in the 

Gulf of Mexico accounts for 

29 percent of total U.S. crude 

oil production, and offshore 

natural gas production in the 

Gulf accounts for 13 percent 

of total U.S. production. The 

effects of this industry on fish 

and fish habitat in the Gulf of 

Mexico include wetland loss 

associated with dredging channels for pipelines and 

transportation, pollution from oil spills both large 

and small, and noise effects on fish and marine 

mammals (whales and dolphins). In contrast to 

these negative effects, retired offshore oil and gas 

platforms are sometimes converted to “artificial 

reefs” that provide additional fish habitat. 

Agricultural runoff 

Each summer in the northern Gulf of Mexico a 

hypoxic (low oxygen) zone forms, primarily the 

result of excess nutrients from Mississippi River 

Basin agricultural runoff into the Gulf of Mexico. 

Excess nutrients enhance algal growth. The algae 

then die and decompose, using up oxygen in the 

process. In 2009 this so-called “Dead Zone” was 

6,600 square miles in size—larger than the state 

of Connecticut. Most aquatic organisms cannot 

survive in habitats with severely low oxygen levels, 

and are forced to move from these areas if they are 

mobile, or die if they are not.

NOAA
Did You Know?

The eastern Gulf of Mexico states had the 

greatest total expenditures in 2006 for 

marine and freshwater recreational fisheries 

of all the regions described in this report. 

More than $6.2 billion was expended for 

marine and freshwater recreational fisheries, 

and an additional $504 million in commercial 

catch occurred in 2009.

Alabama is consistently ranked among the 

top three to five states in terms of overall 

biodiversity, yet half of Alabama’s aquatic 

species are considered endangered or 

threatened. 

The Everglades has been designated as 

a “wetland of international importance” 

by the Ramsar Committee, which selects 

wetlands throughout the world to prioritize 

for conservation.

The eastern Gulf of Mexico states contain 

areas where the natural water flows have 

been substantially altered. South and 

central Florida has been essentially re-plumbed, 

first to support agriculture and flood control and 

more recently to support municipal water demands 

for its growing human population. Louisiana has 

also experienced major changes in hydrology as a 

result of the levees built along the lower Mississippi 

River and channels dredged through the Mississippi 

River Delta. 

Fish Habitat in the Eastern Gulf of Mexico States

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

29

Eastern Gulf of Mexico States (Louisiana, Mississippi, Alabama, Florida)

NOAA
Agriculture is the primary land use in these states, 

with a wide variety of row crops—including sugar 

cane, rice, citrus, and cotton—as well as cattle 

farming. Forestry is the primary agricultural 

activity in Louisiana, with almost 14 million acres 

under management. Overall, the largest percentage 

of rivers in the eastern Gulf of Mexico states is at a 

low risk of current habitat degradation. Areas with 

a high risk of habitat degradation from agriculture 

include central Florida, with its high percentage 

of land in pasture, and southwestern Louisiana, 

where row crops are the major factor contributing 

to habitat degradation. 

Eastern Gulf of Mexico — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45

% Stream Length

15%

17%

27%

39%

2%

Fish with Habitat Trouble

Gray snapper, spotted seatrout, and red 

drum inhabit mangrove forests along both 

coasts of southern Florida. Their habitat is 

under constant threat from development.

Saltmarsh topminnows have been affected 

by the extensive loss of their habitat due to 

wetland fill and conversion of marshes to 

open water.

Blue suckers were once a staple in the diet 

of people living along the Mississippi River. 

They are very rare today, due to habitat 

fragmentation and barriers to this fish’s 

long migration.

The highest percentage of estuarine area in the 

eastern Gulf of Mexico states falls into the moderate 

category of habitat degradation. The Tampa Bay 

estuary is at high risk of habitat degradation due 

to reduced water flows and a surrounding landscape that is highly altered and contains numerous 

sources of pollution.

Human Activities Affecting 

Fish Habitat

Urban land use

Florida contains some of the fastest growing 

counties in the country. Ft. Lauderdale, Orlando, 

West Palm Beach, Pensacola, and Daytona Beach 

rank among the most sprawled cities. Pollution 

and disruption of natural water flows have damaged 

the Florida Keys reef system, degraded fisheries in 

Florida Bay, and are depriving the Everglades and 

its dependent aquatic species of the water they 

need to thrive. Louisiana contains an urbanized 

corridor that reaches from New Orleans west along 

Interstate 10 to Baton Rouge, Lafayette, and Lake 

Charles, and north to Alexandria. The roads and 

development along this urban corridor contribute 

pollutants to the wetlands in the area, including 

the Atchafalaya Swamp.

30

Eastern Gulf of Mexico — Risk of Current Degradation

17%

53%

4%

Very Low

Low

Moderate

High

Very High

9%

17%

% Estuary Area

snapper
sediment build-up, and restoring native vegetation. The inter-tidal oyster reefs improve marine 

habitat diversity and help restore natural vegetative 

barriers to stabilize coastal sediments. The structures are quickly colonized by oysters and mussels, 

which filter the water and provide valuable habitat 

for fish and other marine life. The ongoing project 

has been a success thanks to the leadership of the 

Air Force and support provided by volunteers who 

provided all of the manual labor to install the 

oyster domes and oyster shell bags and to plant 

marsh grass. This project is part of a much larger 

effort by Tampa Baywatch and partners such as the 

Southeast Aquatic Resources Partnership to increase 

oyster habitat and reduce shoreline erosion in the 

Tampa Bay area. In 2007 and 2008 alone, almost 

3,000 oyster domes were installed.

Agriculture

The draining of the Everglades to create the Everglades Agricultural Area is one of the most well 

known examples of the effects of agriculture on fish 

habitat in the eastern Gulf of Mexico. In addition 

to the physical loss of habitat, the agricultural 

activities in this area release sediments and nutrients into Everglades National Park and Florida Bay, 

creating low oxygen zones caused by the decomposition of algae blooms. 

Working for Change

Tampa Bay Shoreline, MacDill 

Air Force Base, Florida

The historical loss of mangroves along the eastern 

coastline of MacDill Air Force Base has left the 

shoreline exposed and subject to severe erosion. 

Construction of near-shore oyster reefs along the 

coastline, which began in 2004, has helped stem 

this erosion by reducing wave energy, encouraging 

Jason Kirkpatrick, MacDill Air Force Base

Jason Kirkpatrick, MacDill Air Force Base Jason Kirkpatrick, MacDill Air Force Base

31
Fish Habitats in the Southern 

Plains States

The southern plains states contain a mixture 

of coastal, desert, and plains habitats. 

Eastern Texas contains large areas at very 

high risk of habitat degradation from the factors 

assessed. In particular, urbanization is having a 

significant effect in the “Texas Urban Triangle” 

between Houston, Dallas/Fort Worth, and San 

Antonio. Smaller areas at very high risk of habitat 

degradation occur in central Oklahoma and northeast Kansas. Regional habitat losses and degradation are attributed principally to the conversion of 

native prairie to agriculture and the diversion of 

water for irrigation. Irrigation diversions on the Rio Grande and Red, 

Arkansas, and Kansas rivers have 

changed the flow in these rivers to the 

point where there are large reaches 

without water seasonally. A range of 

factors affect fish habitat in reservoirs, 

including sedimentation, loss of 

structural habitat, excessive nutrient 

inputs, loss of shoreline habitat, and 

altered water flow. About 31 percent 

of the river miles in the southern 

plains states are classified as being at 

low or very low risk of current habitat 

Did You Know?

The southern plains states ranked third in 

expenditures associated with marine and 

freshwater recreational fishing in 2006. 

These expenditures totaled more than 

$3.9 billion and most were from the state 

of Texas. Texas also brought in more than 

$150 million in commercial catch in 2008.

The Rio Grande begins as a clear spring and 

snow-fed mountain stream at the continental 

divide in Colorado, but due to water 

diversions, it rarely has enough water to 

complete its journey to the Gulf of Mexico.

The population of Texas increased by 21 

percent from 2000 to 2010. Urban areas 

in Texas are projected to double by 2050 

which, without careful planning, will increase 

pollution and negatively affect fish habitat.

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

32

Southern Plains States

(Kansas, Oklahoma, Texas)
USFWS

degradation and about 38 percent are classified as 

being at high or very high risk of current habitat 

degradation.

Southern Plains — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35

% Stream Length

15%

23%

31%

30%

1%

Fish with Habitat Trouble

Large river minnows such as the Rio 

Grande silvery minnow are at significant 

risk due to streamflow modifications, 

loss of connectivity, increased water 

clarity, and establishment of sight-feeding 

predators and competitors. 

All spring-dependent fish are at risk due 

to increasing rates of aquifer withdrawals 

for agriculture and expanding urban 

areas. 

The ongoing loss of tidal wetlands along 

the Texas coast is reducing habitat for 

blue crab, shrimp, speckled sea trout, 

redfish, and other important commercial 

and recreational species.

Two-thirds of the estuarine area in Texas has a high 

or very high risk of habitat degradation due to the 

factors assessed. Galveston Bay was assessed as 

having a very high risk of degradation from land use 

factors (urbanization), but did not have an overall 

high risk of habitat degradation because flushing of 

the Bay reduces degradation from excess nutrients. 

Coastal areas in Texas are becoming increasingly 

urbanized, causing loss of habitat and impaired 

water quality. 

Rio Grande silvery minnow

33

Southern Plains — Risk of Current Degradation

4%

22%

25% 9%

40%

Very Low

Low

Moderate

High

Very High

% Estuary Area

Human Activities Affecting 

Fish Habitat

Agriculture

Wheat and cotton are the two most commonly 

grown crops in the southern plains states. Areas 

with a high risk of habitat degradation in western 

Kansas correspond to areas of these and other 

row crops. Nutrient runoff from crop fields flows 

into streams and eventually ends up in the Gulf of 

Mexico. This high-nutrient runoff contributes to 

the low oxygen dead zone in the Gulf of Mexico, 

described in more detail in the section on the Gulf 

of Mexico. 

Pasture

Cattle and sheep ranching are common in southern 

plains states. Areas of very high risk of habitat 

degradation in eastern Texas correspond to areas 

characterized as pasture. When livestock drink 

from local streams they trample the stream banks 

and create excess sedimentation in the streams.

Urbanization

The southern plains states contain one of the 

fastest-growing urban centers areas in the country—

the triangle of Houston, Dallas/Fort Worth, and 

San Antonio, where 17 million people are spread 

over 58,000 square miles. In these cities and the 

surrounding suburbs, large areas of impervious 

surfaces replace natural streamside habitat, increase 

pollution and sedimentation, and alter hydrology. 

Declining fish populations are the result, near the 
34

cities as well as downstream. Another effect of 

urbanization is demand for water. Urban areas 

in the Texas Urban Triangle initially relied mostly 

on groundwater to meet their water needs, but 

as aquifer levels plummet, more and more cities 

have switched to surface water from streams and 

reservoirs. Major rivers such as the Colorado, San 

Jacinto, and Trinity are already heavily used for 

urban and agricultural water supply, and the San 

Jacinto was named one of America’s Most Endangered Rivers in 1996.

Working for Change

Lake Houston, Texas

Lake Houston is a 12,240-acre reservoir constructed 

on the San Jacinto River by the City of Houston in 

1953 to provide water for municipal and industrial 

purposes. Its location within the Houston metropolitan area results in heavy recreational use. Lake 

Houston supports recreational fisheries for crappie, 

catfish, and largemouth bass. The reservoir is 

suffering from excess sedimentation related to gravel 

dredging in the streams that feed into it. The Texas 

Parks and Wildlife Department is working with the 

City of Houston, the San Jacinto River Authority, 

private interests, and regulatory authorities to find 

solutions to the sedimentation problems at a watershed level. The work will also include constructing 

wetlands in the project area and outreach efforts 

to demonstrate the importance of these efforts to 

the public. This project is one of many the Reservoir Fisheries Habitat Partnership will engage in as 

they further their mission “To protect and improve 

healthy aquatic habitat in reservoir systems for the 

benefit of fish and wildlife and the enhancement of 

quality of life for people and their communities.”

Texas Parks & Wildlife Department, Lake Houston

Texas Parks & Wildlife Department
Did You Know?

More than $406 million was expended 

on freshwater recreational fishing in the 

northern plains states in 2006.

The Ogallala aquifer—the largest aquifer 

in the region—is severely depleted due 

to irrigation for farmlands, which has so 

affected water flow in the Platte River that 

it is now seasonally dry in many reaches.

Fish Habitat in the Northern 

Plains States Fish habitat in the northern plains 

states is relatively undisturbed by 

urban development. Agriculture and 

livestock are the predominant land uses, 

contributing to runoff of nutrients and 

sediment into streams. Southern Nebraska 

has areas with a high risk of habitat degradation due to row crops and road crossings. Central and southeast South Dakota 

have areas with a very high risk of habitat 

degradation due mainly to row crops and 

pasture, and similar areas are found in 

the eastern two-thirds of southwest North 

Dakota. Road crossings and dams also 

contribute to habitat degradation in all 

of these areas. The greatest amount of 

river miles in the northern plains states 

fall into the moderate category of risk of 

current habitat degradation.

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

35

NorthernPlainsStates (North Dakota, South Dakota, Nebraska)

NEBRASKAland Magazine/Nebraska Game and Parks Commission
Fish with Habitat Trouble

Prior to the construction of dams on the 

Missouri River, pallid sturgeon had access 

to hundreds of miles of river to spawn and 

provide for larval drift. These large fish 

are rare today, the result of the substantial 

changes to the Missouri River during the 

past 50 years.

The Topeka shiner once lived in Iowa, 

Kansas, Minnesota, Missouri, Nebraska, 

and South Dakota. It is still present in these 

states, but populations have declined greatly 

due to habitat fragmentation and destruction. 

Human Activities Affecting 

Fish Habitat

Agriculture

Wheat, corn, and soybeans are some of the primary 

crops grown in the northern plains states. In areas 

of intense cultivation, streams are often channelized 

for irrigation, reducing their habitat value for fish 

as temperature, vegetation cover, and stream flow 

are significantly changed. In addition, watersheds 

dominated by row-crop agriculture discharge excess 

sediment and nutrients to downstream waters. In 

many areas, water withdrawal to support agriculture is so severe, dry streambeds result. 

Pasture 

Lands within the watersheds of Great Plains streams 

that are not used for agricultural crops are often 

used for cattle grazing and hay production, leading 

to direct habitat impacts as cattle trample stream 

banks, increasing sedimentation and nutrient loads. 

In addition, cattle watering ponds constructed by 

diverting streams disrupt the connectivity of the 

streams, potentially interfering with the natural 

movements of fish. 

Northern Plains — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40

% Stream Length

6%

29%

36%

24%

5%

Sam Stukel, South Dakota Game Fish Parks

pallid sturgeon

36
Working for Change

Christine and Hickson Dams, North Dakota 

The Christine and Hickson dams are located in the 

upper Red River in Minnesota and North Dakota, 

just south of Fargo. These two low-head (5 feet 

and 7 feet) dams block passage of lake sturgeon, 

walleye, catfish, and many other native river species. 

Through a partnership between several state, 

federal, local, and non-profit agencies in Minnesota 

and North Dakota, the two dams will be replaced 

with rock arch rapids that will allow fish access to 

37 upstream miles and to two upper tributaries. 

This project will be the culmination of a 10-year 

effort to replace all of the low-head dams with rock 

arch rapids, in keeping with the goals and objectives of the Great Plains Fish Habitat Partnership. 

This effort will restore fish passage, increase fish 

and native mussel production, and increase recreational fishing opportunities and boating safety on 

the Red River.

NEBRASKAland Magazine/Nebraska Game and Parks Commission 

37

Sam Stukel, South Dakota Game Fish Parks
Fish Habitat in the Mountain States

I

n general, fish habitat in the mountain 

states ranges from pristine in wilderness 

areas and national parks to degraded 

in urban areas, mining districts, and heavily 

grazed or farmed floodplains. About 64 

percent of the river miles in the mountain 

states are at low or very low risk of current 

habitat degradation. 

Areas with a very high risk of current 

habitat degradation in the mountain 

states correspond to areas of intensive 

agriculture (southern Idaho), urban 

development (Salt Lake City), rivers 

that have been altered for hydropower 

and navigation (the Snake River in Idaho 

and the Colorado River in Utah), or where 

impacts of grazing, hard rock and dredge 

mining, and logging 

have degraded aquatic 

habitats. In addition, 

many of the region’s 

rivers and streams have 

been altered extensively 

for water uses, including 

irrigation for agriculture 

Did You Know?

More than $1.9 billion was expended 

on freshwater recreational fishing in the 

mountain states in 2006.

The mountain states are home to more 

varieties of cutthroat trout than anywhere 

else in the nation.

The Salmon River in Idaho historically 

produced 45 percent of all the steelhead 

trout and 45 percent of spring- and 

summer-run Chinook salmon in the 

Columbia River Basin, but now those 

runs are in serious decline because of the 

effects of hydroelectric dams on the lower 

Snake and Columbia rivers, overharvest, 

hatcheries, and habitat degradation.

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

38

Mountain States

(Colorado, Idaho, Montana, Utah, Wyoming)
Joel Sartore, available through USFWS

and flood control. Introduced fish species have also 

played a part in the decline of native fish species 

in the region. Most recently, energy exploration in 

Colorado, Wyoming, and Utah has brought new 

risks and threats to fish habitat from water diversion and direct habitat loss.

Mountain — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50 55

% Stream Length

7%

10%

19%

50%

14%

Fish with Habitat Trouble

Snake River steelhead, Chinook salmon, 

sockeye salmon, and many other species 

of fish that migrate between freshwater and 

saltwater are in serious decline because of 

the numerous barriers along the Snake River 

and tributaries, as well as barriers outside 

the region along the lower Columbia River. 

Some populations are so low they have been 

listed as threatened or endangered under the 

Endangered Species Act.

Bull trout are in serious decline due to water 

diversion and withdrawal, water temperature 

changes, and barriers to migration. They are 

listed as threatened under the Endangered 

Species Act.

Various sucker species and seven sub-species 

of native cutthroat trout are threatened by 

barriers to migration, water diversion, riparian 

habitat and shading losses, water temperature 

alteration, and direct habitat degradation.

Human Activities Affecting 

Fish Habitat

Agriculture

The agricultural areas of the mountain states have 

created a substantial drain on the water resources 

of this region. Areas where there is a high risk of 

habitat degradation, such as southern Idaho, correspond to areas with a great amount of row crops 

and rangeland. Farms and ranches dependent 

on irrigation require increasing amounts of water 

diverted from streams and rivers, fragmenting the 

watersheds and leaving less water in the streams 

for fish. Agricultural runoff and cattle grazing in 

unprotected areas near streams and rivers degrade 

water quality through direct inputs of nutrients and 

excess sediments, and by altering streamside vegetation and wetlands.

L. Lohr

bull trout

39
Dams

Dams and irrigation diversion structures provide 

power and flood control along the rivers of the 

mountain states, as well as supply water to the farms, 

ranches, and cities in these states. Dams also make 

it difficult, if not impossible, for fish to migrate to 

and from spawning grounds. The reduced flows 

from water diversions result in less water in the 

streams for fish, and they change river habitat by 

changing sediment and woody debris movement. 

The decrease in many species of Pacific salmon in 

the mountain state tributaries to the Columbia 

River is a direct result of barriers to upstream and 

downstream migration of fish compounded by 

other factors such as overharvest and habitat degradation. Similar effects have been documented for 

bull trout, many of the cutthroat trout sub-species, 

Pacific lamprey, and white sturgeon, as well as 

suckers and minnows.

Working for Change

Georgetown Creek, Idaho

Georgetown Creek is a tributary to the Bear River, 

identified by the Idaho Department of Fish and 

Game as a high-priority area for the restoration of 

Bonneville cutthroat trout. Fish biologists have 

tracked migratory Bonneville cutthroat trout into 

lower Georgetown Creek, but barriers block their 

upstream migration. These barriers include three 

impassable culverts under a road through the 

bottom of Georgetown Canyon that not only block 

fish passage, but also are eroding, causing water 

quality and sedimentation problems.

The Georgetown Road Relocation Project, funded 

by the Western Native Trout Initiative, is a multiyear project to move approximately 2 miles of road 

(including the three impassable culverts) from the 

bottom of Georgetown Creek to uplands. The new 

road was built in 2008, and in 2009 the CaribouTarghee National Forest initiated removal of the 

old road. This project has restored water quality 

and habitat through the removal of the old road 

and restored fish passage with a fish ladder to 

allow fish to move around the remaining barriers. 

Efforts are continuing to reconnect other segments 

of the stream. This road relocation project is just 

one component of an overall watershed restoration 

strategy for Georgetown Creek that also includes 

fish passage around a hydroelectric diversion 

headgate on Bureau of Land Management land and 

passage over an irrigation dam on private land. 

US Forest Service, Georgetown Creek

40
Did You Know?

More than $1.2 billion was expended 

on freshwater recreational fishing in the 

southwestern states in 2006.

Desert aquatic habitats support 179 

species of native fish, 54 of which are 

listed under the Endangered Species Act.

Fish Habitat in the Southwestern States

Aquatic habitats in the desert southwest range 

from high-elevation mountain streams to 

the channelized and often dry streambed 

of the Salt River. Springs, seeps, and wetlands are 

oases in the deserts that provide unique and fragile 

habitats. Desert aquatic habitats and desert fish 

species throughout the western United States are 

disappearing due to habitat fragmentation, water 

diversion and loss, and complete habitat destruction. 

Large rivers in the southwest states have been 

greatly affected by the construction of dams and 

diversions that interfere with fish migration, alter 

in-stream habitat characteristics including sediment and 

woody debris movement, 

change water quality and 

temperature, reduce access 

to off-channel habitats, and 

reduce water flows downstream. The reservoirs behind 

these dams support tremendously popular sport fisheries 

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

41

Southwestern States (Arizona, Nevada, New Mexico)
Bruce Taubert, Arizona Game and Fish Depar mt ent

based on introduced species that often outcompete 

and prey upon native desert fish. 

Water projects that include large dams and water 

withdrawal systems alter seasonal flows and 

temperatures, adversely affecting desert species that 

are adapted to the natural cycle. Combined with 

water diversions for domestic and agricultural use, 

extended and ongoing drought conditions in the 

southwest have adversely affected all desert aquatic 

habitats. Water diversions and drought were not 

among the factors assessed, so most of the river 

miles in the Southwestern states fall into the “low” 

and “very low” risk categories of current habitat 

degradation from the factors assessed (urbanization, agriculture and grazing, pollution, mines, and 

dams).

Human Activities Affecting 

Fish Habitat:

Dams and other barriers

Areas with a very high risk of habitat degradation in the desert southwest occur in southwest 

Arizona, where road crossings and dams associated 

with urbanization fragment habitat and interrupt 

fish migration. Large rivers like the Rio Grande 

and Colorado River have been greatly affected by 

dams and diversions, both impediments to fish 

movement.

Agriculture and water use

The agricultural areas of the desert states demand 

ever-increasing amounts of water from an over-allocated regional water supply. Farms dependent on 

irrigation and growing populations use increasing 

amounts of water diverted from streams and rivers, 

Southwestern — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70

% Stream Length

4%

5%

15%

62%

14%

Fish with Habitat Trouble

Habitat for loach minnow and roundtail chub 

has been severely reduced and fragmented, 

resulting in substantial declines in the 

numbers of these fish.

Apache and Gila trout have been greatly 

diminished in their range and numbers 

because of direct habitat loss from 

overgrazing, introduced salmonids, and 

water loss. Recent efforts have stabilized 

their range and some improvements in their 

number have occurred.

Currently 30 percent of desert fish are 

so imperiled they are federally listed as 

threatened or endangered. 

The majority of native desert fish (82 

percent) are endemic to the desert west, a 

testimony to the unique nature of the fauna 

and the habitats on which they depend.

Tom Cappiello

loach minnow 

USFWS

42
leaving less water for fish and impairing connectivity of their habitats. Spring systems are drying 

up due to development of groundwater, as well as 

through physical alterations for the use and diversion of surface water outflows.

Working for Change

Red Rock Cíenega Restoration, New Mexico

“Cíenegas”—wetland habitats unique to the desert 

west—are rapidly disappearing due to changes in 

the availability of groundwater and invasion of 

non-native vegetation. This habitat loss has led to 

severe imperilment of cíenega species, including 

the Gila topminnow and Gila chub. To provide 

habitat for these fish, the New Mexico Department 

of Game and Fish, working with the Desert Fish 

Habitat Partnership, has restored the cíenega in 

the Red Rock Wildlife Management Area near the 

Gila River. The project involved removing nonnative vegetation, planting native vegetation, and 

restoring a groundwater connection to the wetland. 

Additionally, a pump was 

installed to provide an emergency source of water during 

drought years. In 2010, as the 

cíenega habitat recovered, the 

New Mexico Department of 

Game and Fish worked with 

the Arizona Game and Fish 

Department and the U.S. 

Fish and Wildlife Service to 

establish populations of Gila 

topminnow and Gila chub, 

thereby doubling the populations of both species in New 

Mexico. The cíenega will 

provide habitat not only for 

fish, but also for neotropical 

birds, waterfowl, and amphibians. An interpretive trail is also being constructed to increase the 

educational and recreation value of the Wildlife 

Area. This project is one of many that will be 

undertaken by the Desert Fish Habitat Partnership 

as they pursue their mission of “Bringing together 

people and organizations with a common interest 

in voluntary conservation of desert fishes and their 

habitats.”

New Mexico Department of Game and Fish, Red Rock Cíenega Restoration New Mexico Department of Game and Fish, Red Rock Cíenega Restoration New Mexico Department of Game and Fish, Red Rock Cíenega Restoration 

43
Fish habitat in California’s Central Valley, the 

Palouse Hills of southeast Washington, and 

western Washington and western Oregon 

has a high risk of current habitat degradation due 

to row crops and pasture that require substantial 

irrigation. Urban areas such as Los Angeles, San 

Francisco, and the corridor from Eugene through 

Portland to Seattle are also at a high risk of current 

habitat degradation due to urban land use and road 

crossings that do not allow the passage of fish or 

sufficient amounts of water. Habitat in the Cascade 

Mountains, parts of National Forests in eastern 

California and northwest Washington, and southwest Oregon is at low risk of current degradation 

due to the factors assessed. Overall, a majority (58 

percent) of the river miles in the Pacific coastal 

states are at low or very low risk of current habitat 

degradation from the factors assessed. 

Estuaries in central and southern California 

including San Francisco, San Diego, and San Pedro 

bays are at high risk of current habitat degradation due to altered water flows and pollution in the 

surrounding watersheds, but other estuaries in the 

Pacific coastal states have the lowest risk of current 

habitat degradation of all the estuaries assessed. 

Fifty-three percent of the estuarine area in the Pacific 

coast states has a low or very low risk of current 

habitat degradation from the factors assessed.

Did You Know?

In 2008, the Pacific coast states brought 

in more than $490 million in commercial 

fish catch, and had more than $3.8 billion 

in expenditures associated with marine and 

freshwater recreational fishing; these are 

the fourth largest amounts of all the regions 

described in this report. 

Pacific salmon swim immense distances 

in their migrations. For example, Chinook 

and sockeye salmon travel over 900 miles 

and climb nearly 7,000 feet from the Pacific 

Ocean as they return to central Idaho to 

spawn.

Nearly 75 percent of the available water in 

California originates in the northern third of 

the state (north of Sacramento), whereas 

80 percent of the demand occurs in the 

southern two-thirds of the state. 

Fish Habitat in the Pacific Coastal States

Stan Allen

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

44

Pacific Coast States

(Washington, Oregon, California)
Pacific Coast — Risk of Current Degradation

Very Low

Low

Moderate

High

Very High

0 5 10 15 20 25 30 35 40 45 50 55

% Stream Length

16%

9%

18%

49%

9%

Pacific Coast — Risk of Current Degradation

23%

30%

10%

5%

32%

Very Low

Low

Moderate

High

Very High

% Estuary Area

Fish with Habitat Trouble

Many populations of Pacific salmon are in 

serious decline and are listed as threatened or 

endangered under the Endangered Species Act 

due to habitat loss and degradation, barriers to 

migration, overharvest, and other factors.

White and green sturgeon, Pacific lamprey, and 

Pacific smelt populations have declined in much 

of this region from migration barriers, water 

quality degradation, and water diversion.

Many unique species of chub, sucker, and 

pupfish are also in serious decline due to 

the effects of water withdrawals, geothermal 

development, and agricultural pollution, 

including the threatened Warner sucker, 

endangered Borax Lake chub, and several 

endemic Goose Lake fish.

Human Activities Affecting 

Fish Habitat

Dams and agriculture

The rivers of the Pacific coast states are heavily 

altered by dams and diversions. The dams generally are used for hydropower generation, irrigation, 

and transportation, all essential to supporting the 

region’s extensive agricultural and manufacturing 

(aluminum, aircraft, shipbuilding) industries. 

Dams create problems for fish such as salmon and 

steelhead, which live in the ocean as adults but 

reproduce in the upper parts of rivers, by interrupting or halting their migration upstream and 

killing large numbers of young salmon as they 

move downstream through powerhouses or spillways. Numbers of salmon and steelhead have 

declined drastically from historic levels, and many 

populations are listed as threatened or endangered 

under the Endangered Species Act. Dams have also 

reduced the amount of off-channel habitat availNOAA

NOAA

pink salmon

45
able for fisheries, and have reduced connectivity 

between the main river channel and these habitats.

The dams provide water for irrigation and domestic 

water supplies, which directly compete with fish 

for the same water. When changes in rainfall, 

snowmelt, or other factors reduce the amount of 

water in streams, fish can be the first users to feel the 

bite. Water in the western United States is governed 

by a complicated system of water rights that does 

not usually adequately balance the needs of native 

fish with human demands. Accordingly, only a 

few voluntary or litigious efforts to resolve these 

competing-use issues have been successful so far. 

Urban land use

Two of the nation’s 10 largest metropolitan areas 

occur on the California coast: Los Angeles and San 

Francisco. These two areas, along with the Puget 

Sound area, are expected to continue to grow 

rapidly in population and size, increasing the area 

of impervious surfaces and the amount of sewage 

discharge, sediments, and other pollutants associated with urbanization. Los Angeles, which is 

located in a semi-arid plain, affects habitat in the 

Colorado and San Joaquin Rivers through its water 

withdrawals to supply a large urban city via aqueducts. Adjacent to Los Angeles is the Port of Los 

Angeles, originally an area of shallow mudflats 

but now an active commercial deepwater port. A 

large amount of wetlands and other fish habitat 

have been lost and continue to be lost due to port 

expansion and dredging projects throughout the 

Pacific coast states. 

Working for Change

Indian Creek culvert replacement, California

Indian Creek is a tributary to the Mattole River 

in northern coastal California. This tributary 

was once important habitat for coho salmon and 

steelhead, but a culvert near the mouth of Indian 

Creek blocked passage to over 1.5 miles of important spawning and rearing habitat. In September 

2010, the California Fish Passage Forum replaced 

the culvert barrier with a clear span bridge that 

allows unimpeded fish passage upstream and 

natural downstream movement of sediment and 

woody debris in Indian Creek. This project is one 

of many that will be prioritized by the California 

Fish Passage Forum in their strategic plan so that 

funding can be sought to continue opening up 

rivers to fish.

Stan Allen

Robes Parrish

46
Did You Know?

Alaska has 46,882 miles of coastline— 

half of the entire U.S. coastline. 

Alaska commercial fishery catch was 

worth more than $1.3 billion in 2009, 34 

percent of all U.S. commercial catch. In 

2007, Alaska had more than $1.4 billion in 

expenditures associated with marine and 

freshwater recreational fishing.

Alaska produces 62 percent of the 

seafood harvested in the nation, and 

80 percent of the world supply of wild 

sockeye, Chinook, and coho salmon. 

Fish Habitat in Alaska

At 586,412 square miles in area, Alaska is the 

largest state in the United States and has a 

diverse array of fish habitats. Alaska has an 

estimated 46,882 miles of coastal shoreline, more 

than 3 million lakes, and countless rivers that drain 

into a variety of drainage basins. Salmon, pollock, 

halibut, king crab, and many other species support 

robust subsistence, recreational, and commercial 

fisheries. For Alaskans, fishing is an integral part of 

their heritage and culture, and an important means 

of supporting their families.

NOAA

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

47

Alaska 
The assessment of Alaska’s inland fish habitats 

differs from the lower 48 assessment in that data 

limitations allowed only an estimation of the risk 

of habitat degradation based on the amount of 

urbanization, transportation infrastructure, and 

point source discharges (see the Methodology 

section for more details). Due to Alaska’s large size 

and sparse population, 

most of its fish habitat 

is in undeveloped or 

lightly developed 

areas where the 

risk of habitat degradation is low. Fish habitat 

around urban centers has a higher risk of degradation. Protection of Alaska’s intact habitats is a very 

efficient use of limited resources. It is much more 

efficient and effective to protect and restore essentially intact habitats than it is to attempt to restore 

highly degraded areas

A substantial portion of Alaska’s economic activity 

occurs on or around the water, including commercial and recreational fishing, marine transportation, 

oil and gas exploration, mineral mining, and timber 

harvesting and log storage. The extent to which 

these activities negatively affect fish habitat has not 

been thoroughly assessed. An assessment of the 

coastal waters of southeast Alaska was completed 

for this report, using a methodology different from 

either the coastal assessment of the lower 48 states 

or the assessment of Alaska’s rivers. In the map of 

southeast Alaska, each dot on the map represents 

an estuary, with the color indicating which habitats 

are more and less degraded. The assessment results 

indicate that the highest risk of current habitat 

degradation occurs in areas with the highest concentration of roads (including forest roads) and highintensity forest harvest. High amounts of sediment 

in the estuaries are also linked to areas with high 

risk of current habitat degradation. A high risk of 

degraded habitat also is associated with the few 

urban areas such as Juneau, the state capital.

Human Activities Affecting 

Fish Habitat

Urban land use/wetland loss

Forty-three percent of the surface area of Alaska is 

wetlands. On a state-wide basis, less than 2 percent 

of these wetlands have been developed. However, 

in many communities, wetlands may be the only 

land type available for development. In urbanized 

and developed areas of Alaska, such as Anchorage, 

it is estimated that over half of the wetlands have 

been lost to transportation corridor construction, 

utility installation, buildings, and other development projects. Wetland loss fragments habitat and 

5 Very low

4 Low

3 Moderate

2 High

1 Very high

Risk of Current

Habitat Degradation

48
disrupts the migration of fish that use wetlands as 

resting places on their lengthy journeys upstream. 

Wetlands are also critical rearing areas for some 

salmon species. Wetland loss is also linked to 

altered native riparian vegetation, degraded water 

quality, and water flow changes, all of which have 

reached levels that may impair wetland ecosystems 

in the long term. 

streams, reductions in water flow may also affect 

nearshore and estuarine circulation, and in most 

cases the implications of these changes on nearshore fish habitat have not been assessed. 

Resource extraction

Alaska’s economy depends on extraction of natural 

resources such as fish, minerals, and timber. Gold 

and silver, oil and natural gas, and products such 

as gravel are extracted from stream and near-shore 

waters using a variety of methods that have both 

direct and indirect impacts to fish habitats. Timber 

extraction, and the effect of log transfer stations, 

although not analyzed in this assessment, also can 

directly and indirectly affect fish habitats.

Working for Change 

Little Susitna River

Little Susitna River is one of the focal areas for the 

Matanuska-Susitna Basin Salmon Habitat Partnership. In 2008 and 2009, projects supported by the 

Mat-Su Partnership replaced 13 barrier culverts on 

the largest tributaries, opening many miles of new 

habitat in about half of the affected tributaries of 

the river. These projects and those undertaken by 

the other Fish Habitat Partnerships in Alaska (Kenai 

Peninsula Fish Habitat Partnership and Southwest Alaska Fish Habitat Partnership) and Candidate Fish Habitat Partnerships (Pacific Marine and 

Estuarine Fish Habitat Partnership, Salmon in the 

City [of Anchorage], and Salmon Stronghold Fish 

Habitat Partnership) will help ensure that Alaska 

remains a healthy habitat for fish.

Fish with Habitat Trouble

Fish populations in Alaska are generally selfsustaining, healthy, and in the best condition of 

any in the United States. However, substantial 

changes have been noted in the abundance of 

some species of commercial and subsistence 

importance. These include Pacific herring in 

southeast Alaska and Prince William Sound; 

Chinook salmon in Norton Sound, the Yukon 

River, the Nushigak River, and Upper Cook 

Inlet; blue king crab in the Pribilof Islands; Opilio 

tanner crab in the Bering Sea; and red king 

crab in southeast Alaska and around Kodiak 

Island. The life history of each of these species 

includes a near-shore phase during which they 

are vulnerable to land-based pollution and other 

human effects on their habitat. Additional 

factors that have been implicated in these 

declines include large-scale changes in ocean 

circulation, climate change, and overfishing.

Competing freshwater demands

Most of Alaska has an abundance of fresh water, 

but there are an increasing number of demands 

placed on this resource. New hydroelectric projects 

and the expansion of existing facilities increase 

barriers and other adverse effects on streams that 

provide spawning and rearing habitat for salmon. 

Oil exploration and development projects on the 

North Slope withdraw massive amounts of water 

for ice roads and ice pads. In addition to the direct 

impact of water withdrawals from these projects on 

Robert Ruffner

Chinook salmon 

49
Did You Know?

Marine and freshwater recreational fishing 

expenditures totaled more than $110 

million in 2006 and commercial catch 

brought more than $71 million to Hawaii 

in 2009.

The larger native fauna of Hawaiian 

streams include five species of fish, 

two species of mollusks (snails), and 

two species of crustaceans (prawn and 

shrimp). These species are migratory and 

must travel between freshwater and the 

ocean at two vulnerable life stages. 

Fish Habitat in Hawaii

An ancient Hawaiian term, ahupua`a, refers 

to an entire watershed and its associated 

streams, estuary, and near-shore waters, as 

well as the sea out to and including the coral reef. 

An ahupua’a approach to aquatic conservation is 

appropriate in Hawaii because the life cycles of all 

the native freshwater fish, mollusks, and crustaceans include a period of time in the ocean, which 

is strongly affected by runoff and stream discharge 

from land. 

The largest of the eight main Hawaii Islands—

Hawaii, Maui, Molokai, Oahu, and Kauai—have 

well-defined watersheds and perennial streams. 

About 370 perennial streams occur on the five 

largest Hawaiian Islands. Forty large stream systems 

form stream-mouth estuaries at their confluence 

with the ocean. These estuaries are critical transition points for migratory species and represent 

a connecting point between inland and coastal 

systems. They are also important nursery 

habitat for many coastal marine reef 

fish during key life stages. 

Very low

Low

Moderate

High

Very high

Unscored reach

Risk of Current

Habitat Degradation

50

Hawaii 
Gordon Smith

Barrier reefs and fringing reefs surround much of 

the main Hawaiian Islands coastlines, with coral 

atolls predominating in the geologically older 

northwestern Hawaiian Islands, from Nihoa Island 

to Kure Atoll. Often called “the rainforests of the 

sea,” coral reefs support an abundant and diverse 

suite of aquatic species. Large schools of herbivorous fish such as parrotfish and tang feed on the 

algae living on the reef. Some species of tang and 

surgeonfish also feed on decaying plant material. 

Butterflyfish eat the live corals, and wrasse and 

goatfish feed on small invertebrates. Jacks and 

snappers are primarily carnivorous, feeding on 

shrimp, crabs, and other fish. Together, these 

various fish families form an intricate food web 

that is tightly woven into the survival of the reef.

Fish with Habitat Trouble

Freshwater gobies (called o`opu in Hawaiian), 

most of which climb vertical waterfalls, are of 

concern due to loss of habitat, as are shrimp 

of enclosed brackish water bodies known as 

anchialine pools. 

The assessment of Hawaii’s fish habitats differs from 

the lower 48 rivers assessment in that data limitations allowed only a preliminary estimation of the 

risk of habitat degradation (see the Methodology 

section for more details), and only for the watersheds that drain to rivers. Inland aquatic habitats 

in Hawaii have been altered extensively due to 

demands for drinking water and agricultural uses, 

urban development, and flood control. The results 

of the assessment suggest that the areas most at 

risk for habitat degradation coincide with areas of 

urbanization on the islands of Hawaii, Oahu, and 

Maui. 

Human Activities Affecting 

Fish Habitats

Urbanization

Major population centers exist on all of the islands, 

particularly on Oahu which has a densely populated urban core. Urbanization results in physical 

loss of aquatic habitat as well as polluted runoff 

and altered hydrology. Sediment transported from 

urban areas, agricultural lands, and mountain slopes 

is the most damaging pollutant in Hawaiian waters 

because coral reef animals are particularly sensitive to the effects of smothering. Other common 

coastal pollutants are fecal bacteria and nutrient 

contamination, specifically nitrogen and phosphorous runoff. Fecal bacteria from sewage and septic 

systems may sicken swimmers, surfers, and other 

recreational water users. Nutrient contamination, 

often caused by fertilizer runoff, can have a detrimental impact on coastal water quality and damage 

coral reef ecosystems. 

Gordon Smith

o’opu nakea

Gordon Smith

51
Reduced flows

Human-caused modifications to surface and 

ground water systems throughout Hawaii have 

profoundly altered natural hydrologic regimes. 

Fifty-eight percent of perennial streams have 

reduced flows due to water diversions. The original 

inhabitants of the islands diverted streams to 

convert many acres of coastal and valley lowlands 

to taro production; however, the effect of this type 

of water use was probably minimal. In the modern 

era, complex irrigation systems have been built to 

support the cultivation of sugar cane, transferring 

large volumes of water out of natural watercourses 

and into networks of ditches, tunnels, flumes, reservoirs, and, ultimately, to fields. Many structures 

divert all stream water at low to moderate flows, 

leaving the downstream channel completely dry. In 

recent years, regulatory action by state agencies and 

voluntary efforts by some landowners and irrigation system operators have resulted in partial flow 

restoration in a few ecologically important stream 

systems.

Working for Change

Mahuahua `Ai o Hoi Project 

He’eia watershed, Oahu

In the lower He’eia watershed on Oahu, a long 

history of taro and rice cultivation resulted in loss 

of the native wetland vegetation. Agricultural 

production ceased in the early 1900s and since 

then a lack of land management has resulted in the 

current dominance of non-native species within 

the stream, wetland, and estuarine ecosystems, 

which has diminished the extent of suitable habitat 

for a diversity of native plants and animals. The 

Nature Conservancy Hawaii Marine Program and 

the Ko’olaupoko Hawai’ian Civic Club are working 

with the Hawaii Fish Habitat Partnership to restore 

the biological and cultural features of 420 acres of 

lowland riparian, stream, coastal wetland, and estuarine habitat in the He’eia watershed. The project 

will remediate aquatic habitat by restoring native 

vegetation in the wetland; restoring stream banks 

in the lower reaches of the stream and estuary; and 

improving water quality conditions in the wetland, 

stream, and estuary complex. Conservation initiatives that rely on partnerships and cooperation 

among several entities are well accepted in Hawaii. 

The Mahuahua `Ai o Hoi project is only one of many 

that are contributing to the protection and restoration of aquatic habitats in the Hawaiian Islands.

Gordon Smith

52
Aquantitative assessment of marine fish 

habitats of the United States was not 

completed for this report, but will be 

conducted for the 2015 update of this document. 

Marine habitats are well-studied in a few parts 

of the nation, but the condition of most marine 

habitats in U.S. waters has not been studied in 

detail. To facilitate understanding of marine areas 

throughout the world, the United Nations initiated 

a study of Large Marine Ecosystems (LMEs)—large 

areas of ocean, most of them adjacent to the continents—where the production of biological material 

like algae is generally higher than in open ocean 

areas. Six of the 11 LME’s in the United States are 

described below.

Northeast Large Marine Ecosystem

The Northeast LME extends from the Gulf of Maine 

to Cape Hatteras, encompassing 28 major estuaries 

and river systems. It is bounded on the seaward 

side by the Gulf Stream. The combination of circulation patterns in the northern part of the LME and 

nutrient enrichment from estuaries in the southern 

part results in relatively high levels of plankton that 

provide food for menhaden, herring, mackerel, 

sand lance, and butterfish, which in turn become 

prey for larger fish and other marine predators.

The Mid-Atlantic Bight, the southern portion of 

this LME, is a transition zone between the glacial 

till, rocky shores, and steep gradients of the New 

England states and the wide, gently sloping coastal 

plains of the southeastern United States. The coastal 

ocean is a shallow, nutrient-rich, productive environment. Numerous inlets allow larval, juvenile, 

and adult fish to move between estuarine and 

oceanic waters, contributing greatly to the biological productivity of the region.

The Northeast LME supports important commercial 

and recreational fisheries such as haddock, Atlantic 

Did You Know?

Commercial marine fisheries in 2008 

brought in 8.3 billion pounds of fish and 

shellfish valued at $4.4 billion.

American eels spawn in the open Atlantic 

Ocean, in an area known as the “Sargasso 

Sea” (named for all the sargassum 

seaweed that collects there).

The Gulf of Mexico supports “cold seep” 

communities of tube worms, clams, and 

mussels that live off rare species of 

microorganisms that metabolize seeping 

hydrogen sulfide, methane, and other 

hydrocarbons.

53

Marine Waters
cod, summer flounder, winter flounder, and pollock. 

Shortnose sturgeon and Atlantic salmon are listed 

as endangered and populations of anadromous 

species are generally low except for the recent resurgence of striped bass after several years of fishing 

restrictions. American lobster and sea scallops are 

also important fisheries in this area. 

The northeast coast is the most densely populated 

coastal region in the country. Major river systems 

contribute nitrates and phosphates to coastal 

waters from agriculture and sewage. For the LME 

as a whole, water clarity is good but the increasing 

extent of eutrophication (low oxygen levels caused 

by excess nutrients) is cause for concern. Eutrophic 

conditions are predicted to worsen overall based 

on expected increases in nutrients from wastewater, 

septic tanks, agriculture, and urban runoff as the 

coastal population continues to increase. 

Southeast Large Marine Ecosystem

The Southeast LME extends from Cape Hatteras to 

the Straits of Florida, encompassing 18 estuaries 

and river systems and extending seaward to the 

edge of the continental shelf. A dominant feature 

54
of oceanic habitats in the Southeast LME is the 

Gulf Stream, a warm river meandering through the 

ocean along the eastern seaboard to Cape Hatteras, 

North Carolina, where it turns seaward on a transoceanic path toward England. Sometimes the Gulf 

Stream branches to form smaller loops of warm 

water known as “gyres,” of which the Charleston 

Gyre is an example. Gyres are often associated with 

upwelling of nutrient-rich cold water and localized 

short-lived plankton blooms, but the upwelling in 

this LME s not as intense as it is farther north. 

Coral reefs are a habitat of particular significance in 

the Southeast LME. The reefs in Florida include a 

diversity of stony corals, soft corals, sponges, polychaetes, mollusks, crustaceans, echinoderms, fish, 

turtles, and marine mammals. Species associated 

with coral reefs number in the hundreds or even 

thousands.

The estuaries at the landward edge of the Southeast LME provide nursery habitat that promotes the 

production of juvenile fish and shellfish important 

as commercial and recreational species or as prey 

for these species. Major species caught in commercial and recreation fishing include mackerel, swordfish, tuna, Atlantic menhaden, shrimp, crabs, 

sharks, and reef fish.

The Southeast LME has experienced a significant 

loss of wetlands and other shallow-water nursery 

habitat from human activities such as residential 

construction and industrialization. Wetland degradation has also occurred due to the diversion of 

freshwater for agricultural, domestic, and industrial 

uses as well as channeling, dredging, damming, and 

ditching, and the draining of rivers and their floodplains. Coastal development has greatly contributed to the quantity of pollutants in near-shore 

marine waters as well as the deposition of sediments. Eutrophication of many southeastern estuaries is high and is expected to increase in future 

decades.

Gulf of Mexico Large Marine 

Ecosystem

The Gulf of Mexico LME is the largest semienclosed coastal sea of the western Atlantic. About 

30 percent of this LME consists of an extensive and 

topographically diverse continental shelf. Around 

the lower peninsula of Florida the continental shelf 

is primarily carbonate and supports extensive coral 

reefs. In the western Gulf of Mexico southeast of 

Galveston, Texas, two salt domes support an area 

NOAA CCMA Biogeography Branch

55
of brightly colored corals that have been designated 

as the Flower Garden Banks National Marine Sanctuary. In the northern Gulf the continental shelf is 

dominated by mud, but even here offshore petroleum platforms and wrecks create artificial reefs 

that, like naturally occurring ones, attract a diverse 

assemblage of fish and shellfish.

With 47 estuaries, this area is heavily influenced 

by freshwater input, particularly from the Mississippi River which accounts for about two-thirds of 

the freshwater flow in to the Gulf of Mexico. Water 

circulation in the Gulf of Mexico is driven by the 

Loop Current, a warm water current that enters the 

Gulf through the Yucatan Straits. Circulating clockwise in the eastern Gulf, it exits through the Florida 

Straits to become the Gulf Stream. A ring of current 

called the “Loop Current Eddy” often separates 

from the Loop Current, drifting into the western 

Gulf of Mexico where it also circulates water in a 

clockwise direction. These two currents create 

many areas of upwelling and turbulence that serve 

as prime spawning habitat for over 100 families of 

fish.

The Gulf of Mexico LME is considered a moderately productive ecosystem, supporting diverse 

commercial, recreational, and subsistence fisheries. 

Economically important species include shrimp, 

Gulf menhaden, mackerel, grouper, snapper, sea 

trout, and tuna. Commercial catches also include 

large amounts of herring, sardines, and anchovies.

The Gulf of Mexico LME is under considerable stress 

from shoreline development, oil and gas extraction, pollutant discharges, and excess nutrients. 

Wetlands, which are extremely important nurseries 

for shrimp and other species, are undergoing severe 

and continuing losses due to local human activities coupled with global changes such as sea-level 

rise. Coastal Louisiana loses about 16,000 acres 

of wetlands a year, and the entire U.S. Gulf Coast 

lost about 60,000 acres of wetlands a year between 

1998 and 2004.

Estuaries in the northern Gulf of Mexico are characterized by excess nutrients and low oxygen levels. 

The most well known area of low oxygen is the 

so-called “Dead Zone,” an area the size of New 

Jersey where excess nutrients from the Mississippi 

River feed algae blooms that deplete the water of 

oxygen. Fish and other mobile organisms will 

avoid these areas, but bottom-dwelling species 

such as clams and slow-moving crabs are killed 

by the lack of oxygen. Excess nutrients are also 

associated with “Harmful Algal Blooms,” which 

can contaminate fish and shellfish and endanger 

human health.

California Current Large 

Marine Ecosystem

The California Current LME extends along the 

western coast of the United States from southern 

California to northern Washington. It contains 

more than 400 estuaries, bays, and river mouths 

including the Columbia River, San Francisco Bay, 

and Puget Sound. The continental shelf is narrow, 

extending between 5 and 25 miles from the coast. 

Rocky areas in depths less than 130 feet often are 

covered by extensive kelp beds and other marine 

algae, sponges, sea stars, brittle stars, and other 

Texas Parks & Wildlife Department

56
invertebrates. Seaward of the continental shelf and 

slope are complex deepwater habitats including 

seamounts, volcanic ridges, and hot springs, which 

support diverse and often unique fauna.

Circulation is dominated by the southward-flowing 

California Current and the seasonal northwardflowing Davidson Current, which brings warmer 

water close to the coast in the winter. At the 

boundaries between these two major currents and 

other smaller currents, seasonal upwelling of colder 

nutrient-rich waters creates areas of localized high 

productivity. The overall productivity of this LME 

is considered low and varies over a 20- to 30-year 

cycle as the Pacific Ocean shifts between a warm 

regime and a cooler regime, which strongly influences growth and survival of Pacific salmon.

The California Current LME supports numerous 

small fish species such as sardines, mackerel, and 

anchovies as well as larger species including Pacific 

hake, rockfish, sole, lingcod, and five species of 

salmon. Near-shore areas support recreational 

and commercial fisheries for these species as well 

as crabs, shrimp, abalone, clams, scallops, and 

oysters. 

Many Pacific Coast habitats have been dramatically 

altered from their original pristine state. Major 

habitat trends include reductions in freshwater 

flows and access due to dams, estuarine habitat loss, 

damage to seafloor habitats during fishing, and 

increased loading of organic nitrogen compounds 

into coastal waters from urban and agricultural 

runoff. 

The California Current LME is home to a large 

number of anadromous fish species that spawn in 

rivers and streams, so the loss and degradation of 

freshwater habitat in the watersheds adjacent to the 

California Current LME affects the productivity of 

this LME. In the Columbia River basin more than 

half of the streams historically used by salmon 

are no longer accessible due to construction of 

large dams. In the past 10 years, efforts have been 

made to restore access to some of these areas, but 

many, such as those above Grand Coulee Dam, will 

remain inaccessible to Pacific salmon. Estuarine 

habitat in the California Current LME also has been 

dramatically affected by human activities. More 

than 70 percent of the estuarine habitat both in the 

Pacific Northwest and in California has been lost 

or degraded due to diking, filling, polluting, and 

other human activities. As much as 90 percent of 

the coastal wetlands, including bays, estuaries, and 

salt marshes, have been degraded in southern California alone. Other effects on fish habitat in the 

California Current LME include bottom-trawling 

NOAA

57
fishing gear and changes to ocean circulation and 

temperature, which are poorly understood right 

now.

Gulf of Alaska Large 

Marine Ecosystem

The Gulf of Alaska LME extends along the coast of 

southern Alaska and western Canada. It is separated from the California Current LME by the cold 

waters of the eastward-flowing Subarctic Current, 

which divides to form the northward-flowing 

Alaska Current and the southward-flowing California Current. The Alaska Peninsula separates the 

Gulf of Alaska LME from the East Bering Sea LME. 

The Gulf of Alaska LME is considered to be a moderately productive ecosystem whose cold nutrientrich waters support a diverse assemblage of marine 

life. Species of economic importance include crab, 

shrimp, salmon, scallops, walleye pollock, Pacific 

cod, rockfish, and halibut. In addition to commercial fishing, the area supports a large amount of 

recreational and subsistence fishing.

Five species of salmon (Chinook, coho, sockeye, 

pink, and chum) are present in the Gulf of Alaska 

LME. These anadromous fish spend a portion of 

their lives in rivers, streams, and estuaries, so the 

health and productivity of this LME is closely tied 

to human alteration of the landscape. Although 

barriers to fish migration (dams, culverts, etc.) are 

not as widespread in the Gulf of Alaska watershed 

as they are in other parts of the nation, there are 

localized effects near urban centers, transportation 

corridors, and logging operations.

Other ecological problems affecting this LME 

include non-native species (mitten crab, Atlantic 

salmon), industrial and agricultural pollutants, and 

discharges of oil products. The largest tanker spill 

in U.S. history occurred in 1989 when the Exxon 

Valdez went aground off the Port of Valdez, spilling 

11 million gallons of crude oil into Prince William 

Sound. More common than large spills, however, 

are smaller discharges of refined oil, crude oil, and 

hazardous substances.

Pacific-Hawaiian Large 

Marine Ecosystem

The Pacific-Hawaiian LME (technically called the 

Insular Pacific-Hawaiian LME) extends 930 miles 

northwest from the main Hawaiian Islands, encompassing countless islands, atolls, islets, reefs, and 

banks. Lacking a continental shelf, it does contain 

four major estuaries, all within the Hawaiian Islands. 

It is considered a low-productivity ecosystem due 

to the limited nutrients in its oceanic waters, but is 

Stan Allen

58
also a very stable oceanic environment that, unlike 

most other parts of the world’s oceans, has not 

experienced significant warming over the past 50 

years. This LME contains a high diversity of marine 

species, of which 25 to 30 percent are found only in 

this area. It is a major habitat for the North Pacific 

humpback whale.

The most characteristic habitat of the PacificHawaiian LME is coral. Coral reef ecosystems are 

among the most diverse and biologically complex 

ecosystems on Earth, harboring a richness of corals, 

reef invertebrates, and fish, and a variety of other 

flora and fauna. Coral reefs and their associated 

habitats play an important cultural role in the U.S. 

Pacific islands, where community-based conservation, subsistence fisheries, and protected areas have 

been successfully managed for generations.

The Pacific-Hawaiian LME supports commercial, 

recreational, and subsistence fisheries on a smaller 

scale than in the rest of the United States. Species 

of economic importance include tuna, lobsters, 

shrimp, squid, octopus, and armorhead, a fish 

caught only around seamounts.

Trends in fish habitat condition in the PacificHawaiian LME have not been well-studied. Localized degradation of estuarine habitat can be seen 

around developed areas, and most of the shoreline 

of the Hawaiian Islands has been altered. Introduced algal species are becoming a serious concern, 

particularly in the Hawaiian Islands. Intensive 

fishing in and around seamounts may have negative 

effects on these habitats, but little is known about 

this issue. Marine debris is a serious issue but it 

is also almost invisible because the concentrations of floating trash or garbage-choked beaches 

are so remote they are rarely visited by humans. 

Finally, global climate change is a primary concern 

for corals. Two mass coral bleaching events have 

occurred since 2002 and the documentation of 10 

coral diseases throughout the Pacific-Hawaiian LME 

indicates that the health condition of reefs needs to 

be monitored closely.

Summary

Marine habitats of the U.S. encompass more 

than 4 million square miles, the largest Exclusive 

Economic Zone in the world. They range from the 

ice-filled waters of the Arctic Ocean to the tropical 

coral reefs of the Caribbean and Hawaiian Islands, 

providing an array of fish and shellfish as diverse as 

the ecosystems. Most of the productivity of these 

marine areas is concentrated near the coasts, which 

provide habitat for species that migrate to freshwater, in areas of nutrient-rich upwelling, and in 

shallow waters where bottom-dwelling plants and 

animals create complex ecosystems.

Marine habitats near the coast are most likely to 

be adversely affected by human activity. Many of 

the nation’s most productive marine habitats are 

still intact, but many more have become degraded, 

some to an alarming extent, and can no longer 

support the fisheries they once did. Major threats 

to marine habitat include pollution; damage to 

bottom habitat from dredging, fishing gear, or other 

activities; alteration of migration pathways; invasive 

species; marine debris; and climate change. Many 

of these threats can be reduced or avoided through 

sustained proactive efforts locally, but in other cases 

the problems are global and can only be addressed 

through global efforts. If ongoing threats to marine 

fish habitat are not addressed, the productivity of 

U.S. marine habitats is at risk.

Lisa Wedding, NOAA CCMA Biogeography Branch

59
60

Challenges and Opportunities

There are many threats to the health of 

fish habitat in freshwater, estuarine, and 

marine waters throughout the United 

States. Fortunately, many public and private efforts 

are underway to counteract these threats, although 

these efforts are limited by funding, expertise, and 

public understanding. The National Fish Habitat 

Action Plan helps to focus and leverage available 

funds, pool technical expertise, and enlist new 

partners to address the challenges to fish habitat.

Urbanization

More than half of all Americans live in the 39 

largest metropolitan areas (those with populations 

of 1 million or more). Urbanization results in the 

loss of floodplain and natural stream habitat critical 

to the health of freshwater systems. Urbanization 

of the landscape increases impervious surfaces and 

decreases the infiltration of rain and snowmelt 

into the soil, where nutrients and pollution can be 

filtered out. Urban runoff contains oils, fertilizers, 

and detergents, which negatively affect fish habitat 

when washed into adjacent aquatic habitats. 

Increased nutrients can lead to algae blooms and 

low dissolved oxygen, making it difficult for fish to 

survive. Development in floodplains, along lakeshores, and along coasts degrades wetlands that are 

important as fish habitat and as a filter for stormwater runoff. Development in floodplains and 

along coasts removes habitats that protect these 

areas from flooding from storms, storm surges, and 

erosion from river flows and wave action. Development in floodplains and high-hazard coastal areas 

is accompanied by the development of levees and 

seawalls—structures meant to protect these developments that can also exacerbate flooding and 

interrupt key natural processes. 

We cannot erase the effects of urban and suburban 

areas from the landscape, but many efforts are now 

underway to minimize negative effects. Cities are 

implementing programs that encourage residents 

to keep pollutants out of storm drains, to not 

over-use fertilizer, and to plant native vegetation 

along streams. Urban planners are recognizing the 

value of the rivers that flow through their cities and 

are working to restore habitat and fisheries for the 

benefit of urban residents.

Agriculture

Agriculture is a major factor in the degradation of 

fish habitat throughout the country. Depending on 

the type of agricultural practice, negative effects on 

fish habitat can include excess nutrients in rivers and 

estuaries, increased sedimentation, decreased water 

flows when water is diverted for irrigation, physical 

alteration of streams including channelization and 

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61

impoundment, warmer stream temperature, loss 

of woody in-stream habitat, and loss of wetland 

and off-channel habitats. In addition, agriculture 

can convert valuable floodplain areas from natural 

forests and grasslands to farmed fields, decreasing 

the amount of habitats critical to maintaining water 

quality and providing important habitat areas for 

fish and other aquatic organizations. Levees to 

protect farm fields further disconnect floodplains 

from their rivers, depriving freshwater fish and 

other species of access to these valuable habitats 

and disrupting key natural processes on which they 

depend.

Over the past few decades major efforts to reduce 

the loss of fish habitat to agriculture have resulted 

in some gains, but much remains to be done. The 

2008 Farm Bill supports numerous programs to 

help farmers and ranchers conserve soil, water, and 

wildlife. Voluntary efforts such as the Fishers and 

Farmers Fish Habitat Partnership will be essential 

in finding common ground for sustaining agriculture and fish together at a watershed scale. Establishing goals, objectives, and strategies that not 

only target the well-being of fish but the well-being 

and prosperity of farmers is key to keeping soil and 

nutrients on the land, rather than losing them to 

nearby streams and lakes.

Pollution

Pollution from many sources affects fish habitats 

across the country. Some of this pollution is a legacy 

of past industrial practices. Heavy metals and other 

toxins in sediment and the water column threaten 

fish in coastal and river systems. Some polluted 

sediment can be removed through dredging, but 

re-suspension of the pollutants that may occur 

through dredging can create a worse problem than 

leaving the sediments where they are. Pollutants 

from wastewater treatment plants include bacterial 

contamination as well as a wide range of pharmaceutical chemicals whose effects on aquatic organisms are just now being studied.

The Federal Clean Water Act and numerous state 

laws have resulted in major strides toward cleaning 

up the nation’s waters. Created wetland systems 

are being used to remove pollutants from runoff 

and treatment facilities before they enter natural 

systems. Where funds are available, cities are 

converting old stormwater systems to systems that 

pollute less. 

Dams and Other Barriers 

Dams built for industrial use, flood control, irrigation, and energy production are located on rivers 

and streams throughout the country. Dams have 

created thousands of reservoirs that provide recreational opportunities such as fishing, boating, and 

swimming. These structures also create barriers to 

fish migration and interrupt the flow of sediment 

and nutrients downstream, altering fish habitat for 

long distances below the dams. Many old dams 

are obsolete, and no longer serve their original 

purposes. Other barriers to stream flow and fish 

migration include road crossings where culverts 

or bridges are not designed to accommodate the 

natural flow of the river, and tidal gates in coastal 

areas that have similar effects.

Many technologies have been and continue to be 

developed to help fish pass over barriers unharmed. 

Removal of dams is the best solution in cases 

where the cost (both economic and ecological) of 

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62

maintaining the dam outweighs its benefits Local 

citizens and non-governmental organizations have 

been instrumental in getting funding to replace 

culverts and bridges that impede stream flow and 

fish movement. Given the large number of these 

barriers across the country, much more must be 

done to address this source of habitat degradation.

Invasive Species

Fish habitats throughout the United States are 

affected by the introduction of non-native species. 

Some of these introductions, such as salmon in the 

Great Lakes, were purposeful, served a specific goal 

(in this case controlling alewife) and have resulted 

in additional benefits (the salmon sportfishing 

industry in the Great Lakes). Invasive non-native 

species, such as Asian carp, were imported into 

ponds and escaped into natural systems, and still 

others, such as the zebra mussel and giant salvinia, 

were introduced unintentionally through ballast 

water or other pathways.

Aquatic invasive species have negative impacts on 

ecosystems, economies, and, in some cases, human 

health. Control of zebra mussels, one of the bestknown invasive aquatic species, cost municipalities 

and industries tens of millions of dollars. Mitten 

crabs are a well-known species on the West Coast, 

threatening dikes and levees with their burrows and 

competing with native crayfish.

Prevention and control are necessary to prevent 

invasive species from causing additional damage 

to aquatic ecosystems. Public outreach and education are substantial parts of the solution, because 

many invasive species are spread through contaminated boats and waders. Effective regulations on 

the release of ballast water are also needed.

Climate Change 

A changing climate affects water resources and fish 

habitats in many ways. Many scientific studies 

conclude that the current and future effects of 

ongoing climate change include rising sea level; 

warmer temperatures in streams, lakes, and reservoirs; changing patterns and amounts of rainfall 

and snowfall; and increasing acidity in the ocean.

Sea-level rise will erode coastal habitats and push 

saltwater into coastal freshwater resources. Thousands of acres of coastal freshwater marsh, salt 

marsh, and sea grass beds that are home to egg, 

larval, and juvenile stages of commercial and game 

fish will be affected. Higher water temperatures in 

streams, lakes, and reservoirs may lead to the loss 

of cold-water fish communities and the northward 

expansion of warm-water fish communities.

Models of climate change reviewed by the U.S. 

Geological Survey predict that most western states 

will experience less rainfall and more frequent 

drought conditions. Competition for water, 

already extremely contentious, will increase as 

supplies diminish. Reduced snowpack in the west 

and northeast United States will change the flow 

patterns and amount of water in streams and may 

have substantial impacts on reservoirs.

The challenges posed by climate change are great, 

but much can be done to build resilience to the 

effects of global warming. Protecting high-quality 

habitats and healthy fish populations will help fish 

adapt to changing habitat conditions imposed by a 

changing climate.

Texas Parks & Wildlife Department
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Methodology 

The goal of the national assessment was to 

estimate disturbance levels to fish habitats 

in rivers and estuaries from information 

about human activities occurring in the watersheds and the local areas affecting each aquatic 

habitat. This approach is supported by a large 

body of scientific research showing that human 

disturbances to the land transfer to receiving waters 

and contribute to disturbance in downstream fish 

habitats in rivers, estuaries, and the ocean. While 

the specific analytical approaches used to assess 

habitats in the lower-48 states, Alaska, Hawaii, and 

U.S. estuaries differed slightly, the end product of 

each analysis was similar-an estimate of the risk 

that discrete habitat units will be degraded due to 

current human activities on the landscape.

Methods for Rivers Assessment—

Lower 48 States 

The objective of the national assessment of fish 

habitat condition in rivers was to estimate relative 

habitat condition in all river habitats of the United 

States. The large geographic scope of this task 

necessitated a landscape assessment approach 

where mapped information about the state of 

human conditions in the watersheds that drain to 

fish habitats were used to infer the condition of 

habitats for fish life. The approach for estimating 

habitat conditions in the lower 48 states relied on 

information about how measures of fish abundance 

respond to human activities in watersheds affecting 

their habitats. We identified a set of fish “indicators” that are sensitive to habitat conditions, and 

then judged how these indicators responded to the 

different disturbance variables in our analysis (land 

uses, densities of point source pollution sites, dams, 

roads and road crossings, population, and mines) 

using graphical plots of the indicator (vertical axis) 

versus each disturbance (horizontal axis). From 

each plot, we extracted two thresholds representing 

the levels of disturbance at which fish abundances 

show clear responses to disturbance (Fig. 1). The 

first threshold is the level of disturbance at which 

“good” conditions decline for an indicator (Fig. 1, 

purple). The second threshold was the disturbance 

value beyond which the indicator disappears from 

the system (Fig. 1, red). We used these thresholds 

to create a five-point scoring system where ranges 

of each disturbance are assigned condition scores 

according to the indictor state that can be expected 

at each level of disturbance. We scored each river 

segment for 3 to 8 fish indicators in different 

Fig. 1. Scatter plot of a fish indicator versus one 

landscape stress, showing upper (purple) and lower 

(red) condition thresholds and the scoring system 

(colored bars and numbers at bottom).
64

the disturbance class indices. A cumulative disturbance index allows for a first examination of spatial 

patterns of cumulative landscape disturbance to 

habitats.

Methods for Estuary Assessment—

Lower 48 States

For the assessment of estuaries in the lower 48 

states, national datasets of disturbance variables 

measured within estuaries and their surrounding 

watersheds were assembled and mapped using a 

modified version of NOAA’s Coastal Assessment 

Framework, a spatially explicit framework that 

incorporates estuarine water bodies, state and 

federal marine waters not associated with estuaries, 

and their surrounding watersheds. Disturbance 

variables were screened for data quality and spatial 

coverage and were combined into four disturbance categories (river discharge, pollution, eutrophication, and land cover). Multiple component 

datasets often contributed to each category. “River 

discharge” included trends of river flow magnitude 

and pulse duration and density of dams. “Pollution” summarized the density of point source pollution sites including National Pollution Discharge 

Elimination Sites, Toxic Release Inventory sites, 

National Superfund sites, and mines. “Eutrophication” summarized measurements of chlorophyll 

a concentrations, occurrence of algal blooms, and 

dissolved oxygen and nutrient levels. “Land cover” 

summarized percent coverage and trends of urban, 

agricultural, and wetland land cover. 

regions of the U.S. to accommodate the natural 

differences in fish found in different places. This 

yielded between 3 to 8 estimates of condition corresponding to the sensitivity of different fish groups 

to landscape disturbance. The final habitat condition score equaled the average condition score for 

all indicators for each river segment in a region.

Methods for Rivers Assessment—

Alaska and Hawaii

Limited data availability in Alaska and Hawaii 

led to a different assessment approach for these 

states. In Hawaii and Alaska we created risk indices 

for classes of major landscape disturbance (e.g., 

urban, agriculture, point sources, etc.) according 

to data availability in each state, and combined 

these into estimates of “cumulative risk”. Each 

risk index contains a score for each habitat unit 

that ranges from 0 to 1 and represents that unit’s 

degree of landscape disturbance relative to all other 

units (1 = highest disturbance). Index values were 

constructed by either summing similar disturbance 

types in watersheds (e.g., percent row crop agriculture plus percent pasture) and rescaling them from 

0 to 1, or using statistical approaches to combine 

disturbances when many variables were present. 

Cumulative risk index values are the sum of all of 

USFWS
65

Component datasets were combined either by 

direct summation if the datasets were similar or 

statistical approaches to create one index for each 

of the four disturbance categories in each estuary. 

These four disturbance indices were rescaled from 0 

to 100 by calculating the percent rank (a score of 0 

was assigned for estuaries with the highest degree of 

disturbance and 1 for the lowest disturbance). The 

combined score for each estuary was calculated by 

taking the geometric mean of the four disturbance 

indices (a disturbance score of zero was reassigned 

a value of one half the next lowest score so it could 

be included in the geometric mean calculation), 

which was then rescaled from 0 to 100 by calculating the percent rank. Due to data limitations, 

not all estuaries had an index for all four disturbance categories, so a combined score was assigned 

only when the estuary had at least three of the four 

disturbance indices. For the report maps, the final 

scores were divided into equal quintiles: 0-20 (very 

high risk of degradation), 20-40 (high risk of degradation), 40-60 (moderate risk of degradation), 

60-80 (low risk of degradation), 80-100 (very low 

risk of degradation). 

Methods for Estuary Assessment—

Southeast Alaska

The approach for assessing estuarine areas in southeast Alaska differed from the estuarine assessment 

for the rest of the country in a number of ways. 

NOAA’s Coastal Assessment Framework was not 

available for Alaska, so an independent spatial 

framework had to be developed using 12-digit 

HUCs, elevation, and bathymetry to define estuarine and coastal drainage areas. Because of data 

limitations, the Alaska analysis used three categories instead of the four used in the rest of the 

United States. One of these was a land cover/

land use category comprising eight variables: four 

urbanization variables (open, low, moderate, and 

high), two agricultural variables associated with 

timber production (moderate and high), and two 

land protection variables (protected and wilderness 

area). The second category combined five water 

quality variables with sediment toxicity. The final 

category was scores of river flow alteration. Only 

the land cover/land use dataset had sufficient spatial 

coverage for statistical analysis using Principal 

Components Analysis. The other two datasets were 

converted to percentile ranking. The indices from 

the land cover/land use analysis were converted to 

a percentile rank for each coastal unit. Combined 

scores for each unit were only assigned when a unit 

had scores for two or more sub-indices. Combined 

scores were calculated as the mean of the indices.
66

Suggestions for Further Reading

Abell, R., and 27 others. 2008. Freshwater Ecoregions of the World: A New 

Map of Biogeographic Units for Freshwater Biodiversity Conservation. 

BioScience 58(5): 403-414. doi:10.1641/B580507 

http://www.feow.org/

Allan, J. D. 2004. Landscapes and riverscapes: The influence of land use on 

stream ecosystems. Annual Review of Ecology Evolution and Systematics 

35: 257-284.

Annear, T., I. Chisholm, H. Beecher, A. Locke and 12 other authors. 2004. 

Instream flows for riverine resource stewardship, Revised edition. Instream 

Flow Council, Cheyenne, Wyoming. 268 pp.

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. NOAA Coastal Ocean Program Decision Analysis Series 

No. 26 National Centers for Coastal Oceans Science, Silver Spring, MD. 322 pp. 

http://ccma.nos.noaa.gov/publications/eutroupdate/

Carlisle, D.M., D.M. Wolock, and M.R. Meador. 2010. Alteration of streamflow 

magnitudes and potential ecological consequences: a multiregional assessment. Frontiers in Ecology and the Environment. Front Ecol Environ 2010; 

doi:10.1890/100053. 

http://www.esajournals.org/doi/pdf/10.1890/100053

Fausch, K. D., C. E. Torgersen, C. V. Baxter and H. W. Li. 2002. Landscapes 

to riverscapes: bridging the gap between research and conservation of stream 

fishes. Bioscience 52: 483-498.

Gergel, S. E., M. G. Turner, J. R. Miller, J. M. Melack and E. H. Stanley. 2002. 

Landscape indicators of human impacts to riverine systems. Aquatic Sciences 

64: 118-128.

Jelks, H.L., S.J. Walsh, N.M. Burkhead, C. Contreras-Balderas, E. Diaz-Pardo, 

D.A. Hendrickson, J. Lyons, N.E. Mandrak, F. McCormick, J.S. Nelson, S.P. 

Platania, B.A. Porter, C.B., Renaud, S.S. Schmitter, E.B. Taylor, and M.L. Warren, 

Jr. 2008. Conservation Status of Imperiled North American Freshwater and 

Diadromous Fishes. Fisheries, 33:8, p 372-407. 

http://www.fisheries.org/afs/docs/fisheries/fisheries_3308.pdf

Kimbrough, K.L., W.E. Johnson, G.G. Lauenstein, J.D. Christensen, and D.A. 

Apeti. 2008. An Assessment of Two Decades of Contaminant Monitoring in 

the Nation’s Coastal Zone. NOAA/NOS Center for Coastal Monitoring and 

Assessment, Silver Spring MD. NOAA Tech. Memo. NOS NCCOS 74. 105 pp. 

http://ccma.nos.noaa.gov/stressors/pollution/nsandt/welcome.html.

Liu, J. and W.W. Taylor editors. 2002. Integrating landscape ecology into 

natural resource management. Cambridge University Press, Cambridge, UK. 

480 pages.

National Fish Habitat Action Plan. 2006. www.fishhabitat.org

National Marine Fisheries Service. 2010. Marine fisheries habitat assessment 

improvement plan. Report of the National Marine Fisheries service Habitat 

Assessment Improvement Plan Team. U.S. Dep. Comme., NOAA Tech. 

Memo. NMFS-F/SPO-108, 115 p. http://www.st.nmfs.noaa.gov/st4/documents/

habitatAssessmentImprovementPlan_052110.PDF
67

National Marine Fisheries Service, 2009. Our Living Oceans: Habitat. Status 

of the habitat of U.S. living marine resources. Policymakers’ summary, 1st 

edition. U.S. Department of Commerce, NOAA Tech. Memo, NMFS-F/SPO-83, 

32 pp. http://www.habitat.noaa.gov/pdf/our_living_oceans_habitat_tm83.pdf

National Research Council 1991. Restoration of aquatic ecosystems : science, 

technology, and public policy. National Academy Press, Washington, DC. 552 

Pages.

Postel, S. and B. Richter. 2003. Rivers for Life: Managing Water for People and 

Nature. Island Press, Washington, DC.

Silk, N. and K. Ciruna. 2005. A Practitioner’s Guide to Freshwater Biodiversity 

Conservation. Washington, D.C.: Island Press.

Smith, M.P., R. Schiff, A. Olivero, and J.G. MacBroom., 2008. THE ACTIVE 

RIVER AREA: A Conservation Framework for Protecting Rivers and Streams. 

The Nature Conservancy, Boston, MA. 

http://www.conservationgateway.org/file/active-river-area-conservation-frameworkprotecting-rivers-and-streams

U.S. Environmental Protection Agency. 2008. National Coastal Condition 

Report III. U.S. Environmental Protection Agency, Office of Water and Office 

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owow/oceans/nccr3/downloads.html

Waddell, J.E. and A.M. Clarke (eds.). 2008. The State of Coral Reef Ecosystems 

of the United States and Pacific Freely Associated States: 2008. NOAA Technical Memorandum NOS NCCOS 73. Silver Spring, MD. 569 pp. http://ccma.

nos.noaa.gov/ecosystems/coralreef/coral2008/welcome.html

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68

Acknowledgements

Assessment Team

Michigan State University Inland Assessment Group

Dana Infante, coordinator (Department of Fisheries and Wildlife, MSU) 

Peter Esselman (Department of Fisheries and Wildlife, MSU)

Lizhu Wang (Institute for Fisheries Research, Michigan Department

of Natural Resources and University of Michigan)

William W. Taylor (Department of Fisheries and Wildlife, MSU)

Arthur Cooper (Department of Fisheries and Wildlife, MSU)

Ralph Tingley (Department of Fisheries and Wildlife, MSU)

Jacqueline Fenner (Department of Fisheries and Wildlife, MSU)

Dan Wieferich (Department of Fisheries and Wildlife, MSU)

Darren Thornbrugh (Department of Fisheries and Wildlife, MSU)

Jared Ross (Department of Fisheries and Wildlife, MSU)

National Oceanic and Atmospheric Administration 

Coastal Assessment Group

Kirsten Larsen, coordinator (NOAA Fisheries, Office of Science and Technology)

Kristan Blackhart (NOAA Fisheries Service, Office of Science and Technology)

Ken Buja (NOAA Ocean Service, National Centers for Coastal Ocean Science)

Allison Candelmo (NOAA Fisheries Service, Northeast Fisheries Science Center)

Correigh Greene (NOAA Fisheries Service, Northwest Fisheries Science Center)

Hiroo Imaki (NOAA Fisheries Service, Northwest Fisheries Science Center)

Kay McGraw (NOAA Fisheries Service, Office of Habitat Conservation)

Katharine Miller (NOAA Fisheries Service, Alaska Habitat Conservation Division)

David Moe Nelson (NOAA Ocean Service, National Centers for Coastal Ocean 

Science)

Joe Nohner (NOAA Fisheries Service, Office of Science and Technology)

Thomas Noji (NOAA Fisheries Service, Northeast Fisheries Science Center)

Patrick Polte (formerly NOAA Fisheries Service, Northwest Fisheries Science 

Center)

Writing Team

Susan-Marie Stedman, coordinator (National Oceanic and Atmospheric 

Administration)

Tom Busiahn (U.S. Fish and Wildlife Service)

Gabrielle Canonico (National Oceanic and Atmospheric Administration)

Christopher Estes (Alaska Department of Fish and Game, retired)

Janine Harris (National Oceanic and Atmospheric Administration)

Matt Menashes (Association of Fish and Wildlife Agencies)

Ryan Roberts (Association of Fish and Wildlife Agencies)

Mike Stone (Wyoming Game and Fish Department)

Gary Whelan (Michigan Department of Natural Resources and the Environment)

Krystyna Wolniakowski (National Fish and Wildlife Foundation)

The National Fish Habitat Board would like to acknowledge the following 

individuals who contributed to the national fish habitat assessment and 

to this report. The Board would also like to thank the many people who 

reviewed and commented on the report.
69
www. fishhabitat . org