1

Draft copy: 12 Mar 09

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Our Living Oceans:

Habitat STATUS OF THE HABITAT OF

U.S. LIVING MARINE RESOURCES

Policymakers’ Summary, 1st Edition
1
Our Living Oceans: Habitat
This publication may be cited as follows:

NMFS. 2009. Our living oceans: Habitat. Status of the habitat of U.S. living marine resources.

Policymakers’ summary, 1st edition (rev. Oct. 2009). U.S. Dep. Commer., NOAA Tech. Memo.

NMFS-F/SPO-83, 32 p.

An online version of this publication is available at http://spo.nwr.noaa.gov/TM83.pdf.

Certain photographs in this publication are under the copyright protection of the photographers and/or

their employers. These are marked with the copyright symbol ©. Only photographs credited to an

agency of the U.S. Government are in the public domain.

Front cover photographs: top left, table coral and bluestripe snapper, French Frigate Shoals, NWHI, Jean

Kenyon, NMFS; top right, Grand Bay National Estuarine Research Reserve, P. R. Hoar, NESDIS; bottom,

harbor seals in Puget Sound, © OceansArt.us.

Rear cover: top to bottom, left to right: conch in Florida seagrass bed, Heather Dine, Florida Keys

National Marine Sanctuary; North Carolina coast, NOAA; Port of Seattle, NOS, NOAA; Southeast Alaska

wetland and estuary, Mandy Lindeberg, NMFS; right whale, NOAA; green sea turtle, Hawaii, © Ursula

Keuper-Bennett & Peter Bennett; mangrove roots and fish, Elliott Key, Florida, © Jiangang Luo,

University of Miami; Pacific intertidal zone, Nancy Sefton, Olympic Coast National Marine Sanctuary;

squarespot rockfish, Pacific Coast, Mary Yoklavich & Waldo Wakefield, NMFS.

Opposite page: fish and mangrove roots, Elliott Key, Florida, © Jiangang Luo, University of Miami.

Printed with soy-based

ink on recycled paper.
Status of the Habitat of U.S. Living Marine Resources

May 2009 (revised October 2009)

NOAA Technical Memorandum NMFS-F/SPO-83

U.S. Department

of Commerce

Gary Locke

Secretary of Commerce

National Oceanic and

Atmospheric Administration

Jane Lubchenco

Under Secretary of Commerce

for Oceans and Atmosphere

National Marine

Fisheries Service

James W. Balsiger

Acting Assistant Administrator

for Fisheries

© Jiangang Luo, University of Miami

Policymakers’ Summary, 1st Edition

Our Living Oceans: Habitat
FOREWORD

Our Living Oceans: Habitat. Status of the Habitat of U.S. Living Marine Resources joins editions

on living marine resources and economics as the

third and final part of the Our Living Oceans publication series. Taken together, the volumes in this

series serve as a report card on the state of U.S.

living marine resources, their economic contributions to the Nation, and the condition of their

habitats and availability of habitat use information. This Policymakers’ Summary, an abridged

version, and the complete Our Living Oceans:

Habitat report provide the foundation for more

targeted research and comprehensive and detailed

reports in the future.

The most important laws governing activities

of the National Marine Fisheries Service (NMFS)

pertinent to habitat are the Magnuson-Stevens

Fishery Conservation and Management Act

(MSFCMA), recently reauthorized in 2006, and

two laws on protected species, the Endangered

Species Act (ESA) and Marine Mammal Protection Act (MMPA). The MSFCMA includes provisions to help manage and protect Essential Fish

Habitat (EFH) which is defined as “. . . those waters and substrate necessary to fish for spawning,

breeding, or growth to maturity” for commercially

and recreationally harvested fish and invertebrates

within the U.S. Exclusive Economic Zone (EEZ,

typically 3–200 nautical miles from shore). The

ESA as it applies to NMFS includes provisions to

help conserve ecosystems and habitats required by

those marine species threatened with, or in danger of, extinction (e.g. listed fish, invertebrates,

sea turtles, marine mammals, and marine plants).

The MMPA places restrictions on any habitat alteration that could adversely impact a marine

mammal by disrupting behavioral patterns. This

report covers the habitats of all species managed

or protected by NMFS under the MSFCMA, ESA,

and MMPA.

That this report is the first comprehensive

nationwide review of the status and trends of these

habitats, as well as the first comprehensive summary of information available on habitat use at

the fishery management or species-group level, underscores the difficulty of the task. In addition to

cataloging what is known about our Nation’s

aquatic habitats and the patterns of their use by

living marine resources, the report also indicates

what remains unknown. This will help to guide

and prioritize research to address the most important gaps in knowledge. Recent technological advances in autonomous underwater vehicles,

multibeam sonar, and satellites have increased our

ability to fill in these gaps in habitat knowledge.

Our living marine resources are in various

states of condition, ranging from heavily overfished

or endangered through very healthy and functioning at a high level of productivity. Although the

habitat needs of aquatic species often compete with

other societal needs, NOAA must ensure that the

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quantity and quality of available habitat is sufficient to support each life history stage of every

managed species at sustainable levels. There remains considerable scientific uncertainty in quantifying the habitat needs of many species, but there

is substantial evidence that habitat degradation or

loss may be constraining some populations.

This report should not be interpreted as one

of despair nor of unbounded optimism. Federal

and state governments have provided considerable

protection by regulating pollution and development activities, and the increasing availability of

habitat information is contributing to improved

fishery and ecosystem-based management. However, the ever-increasing concentration of humans

along the coasts, growing runoff from cities and

agriculture, and changing climate continue to place

pressure on aquatic habitats. The information provided in this report will give readers a chance to

assess the current situation facing aquatic habitats

and to consider the opportunities that we have

today to protect the habitat that remains and repair or restore habitats that have been degraded or

lost.

Many scientists throughout the National Marine Fisheries Service and many other organizations contributed to this report. As in any complex undertaking being pursued for the first time,

the process was arduous and time-consuming. I

extend my appreciation and compliments to all.

v

James W. Balsiger, Ph.D.

Acting Assistant Administrator for Fisheries

National Marine Fisheries Service

Silver Spring, Maryland

May 2009
PREFACE

This Policymakers’ Summary is an abridged version of the inaugural edition of Our Living Oceans:

Habitat. Status of the Habitat of U.S. Living Marine Resources. The full report serves as a companion report to the two other reports in the Our Living Oceans series: Our Living Oceans. The Economic

Status of U.S. Fisheries and Our Living Oceans.

Report on the Status of U.S. Living Marine Resources.

By presenting an initial assessment of the status

and health of marine and coastal habitats important to living marine resources, the current edition completes the picture of marine resource status begun in the other two reports.

Our Living Oceans: Habitat. Status of the Habitat of U.S. Living Marine Resources represents the

first comprehensive national summary of habitat

information and will serve as a baseline on habitat

knowledge and status for future comparisons. Included are the habitats of commercially and

recreationally harvested fishes and invertebrates,

as well as marine mammals, sea turtles, and other

protected marine species.

The full report consists of three sections: an

Introduction, a National Summary, and the Regional Summaries. The Introduction details the

importance of habitat, the legislation under which

Federal work is conducted, and the current status

of habitat research. The National Summary provides an overview of the status and trends of habitats under the jurisdiction of the National Marine

Fisheries Service, and covers items common to all

regions. The Regional Summaries include more

detailed information about habitat in each region.

This summary of the report presents key information in a concise form. The initial sections

provide the highlights of the full report’s Introduction and National Summary. Instead of regional summaries, the rest of this version consists

of overviews of seven major issues affecting the

habitats of living resources entrusted to the National Marine Fisheries Service’s protection. For

each of these issues, information is provided on

the impacts to habitat, impacts to living marine

resources, and solutions.

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CONTENTS

iv

vi

1

5

7

9

10

13

14

16

18

20

22

24

26

28

30

Foreword

Preface

Executive Summary

Introduction

Scope and Habitat Use

Habitat Status and Trends

Information Quality and Research Needs

Issues Affecting Habitat

Issue: Pollution and Water Quality

Issue: Alteration and Degradation of Rivers and Migratory Pathways

Issue: Fragmentation and Loss of Estuarine and Shallow Marine Habitat

Issue: Fishing Effects on Habitat

Issue: Climate Variability and Change

Issue: Invasive Species and Marine Debris

Issue: Vessel Traffic and Noise

Conclusions

References Cited and Additional Information

vii

1

In 2006, commercial and recreational fisheries supported over 2 million jobs and contributed

over $73 billion to the United States gross national

product, making our Nation one of the largest seafood-producing countries in the world. However,

habitat loss and degradation, including poor water quality; overfishing; and natural environmental changes have put increasing pressure on our

living marine resources, including coastal, oceanic,

and anadromous (species that spawn in fresh water but grow to maturity in salt water, such as

salmon) resources, threatening the sustainability

of the Nation’s fisheries and protected resources.

Ending overfishing in 2010–11, as stipulated in

the Magnuson-Stevens Reauthorization Act

(MSRA), will end one threat to fisheries resources.

Nonetheless, much needs to be done to ensure the

sustainability of the habitats upon which these living resources depend.

The MSRA mandates that the National Oceanic and Atmospheric Administration’s (NOAA)

National Marine Fisheries Service (NMFS) designate Essential Fish Habitat (EFH) and minimize

the effects of fishing and non-fishing activities on

EFH. The Act defines EFH as “. . . those waters

and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity.” In recent

years, momentum has been building for a shift in

fisheries management towards more holistic ecosystem approaches. This includes a broader focus

on ecological relationships and processes, and on

interactions with humans. Habitat is a key component of an ecosystem approach to management.

The Our Living Oceans: Habitat report provides the first national summary of the status and

trends of the habitats used by the living marine

resources under NMFS purview. The report covers the habitats occupied by fishery stocks and

Mangrove roots provide vital habitat for many species,

especially young fish.

© Jiangang Luo, Univeristy of Miami

EXECUTIVE SUMMARY
2

protected marine mammals and sea turtles, ranging from inland streams where anadromous species spawn, to the marine waters of the U.S. Exclusive Economic Zone (EEZ) bounded by the 200

nautical mile (n.mi.; 370 km) limit and beyond.

Nearly all of these animals use shallow marine and

oceanic habitats at some stage of their life cycle.

Many also use estuarine habitats, including many

commercially valuable species. In keeping with

NMFS’s marine focus, fewer species use freshwater habitats, the major exception being anadromous species, such as salmon.

The overall message is mixed. Clearly the

United States still possesses considerable functioning habitat that supports populations of protected

species as well as substantial harvests of fishery

resources. However, it is also clear that there has

been substantial loss and degradation of habitat,

especially where human activities occur. The cumulative impacts of these losses cannot readily be

quantified, but they are undoubtedly considerable,

especially in urbanized watersheds, estuaries, and

coastal areas.

Although the issues affecting U.S. living marine resource habitats vary throughout the country, many are widespread, even if the impacts of

some may be manifested differently in different

regions. Certain issues are important in all aquatic

habitats, while others have more specific and limited impacts within a certain habitat type. The

quantity and quality of the water in many freshwater habitats have been declining for over a century. Changes in land use, industrialization, residential expansion, point and non-point source

pollution, and dams and other flood-control structures are major contributing causes. Estuarine

habitat has been dramatically impacted by many

of the same factors. Nutrient pollution and the

resulting eutrophication, and the continued loss

of estuarine and coastal wetlands and submerged

aquatic vegetation are of particular concern. Shallow marine and oceanic habitats generally have

good water quality, and relatively little habitat has

been lost to human activities. Nevertheless, there

are localized problems and concerns, such as the

Gulf of Mexico “dead zone” where the water underlying the Mississippi River plume contains little

or no oxygen during the summer; the uncertain

effects of long-term climate change; and the impacts of some fishing gear, particularly bottom

trawls, on seafloor habitats.

As the U.S. population continues to grow,

there is increasing pressure on the environment to

provide humans with food, income, recreation,

and other resources. This is especially evident in

coastal areas, where human population growth is

about five times faster than the rate inland. Use of

aquatic habitats will of course affect those habitats, and society faces many choices, including how

to responsibly manage growth, development, and

resource use. To do this wisely, society and decisionmakers must understand the consequences of

their decisions, including the potential for habitat

impacts. In situations where habitat impacts cannot be avoided, decisionmakers must consider

ways to reduce or mitigate impacts and to restore

damaged habitats.

Scientific information is key to effectively

managing habitat. Understanding the relationships

between species and habitats, knowing where and

how much habitat exists, and rigorously monitoring and assessing its condition can provide the scientific basis for managing habitat. However, this

information is only effective in informing public

policy when it is communicated to resource managers, stakeholders, and the public in a timely

manner and in forms that are appropriate to the

specific audiences.

For our Nation to continue benefitting from

abundant living marine resources, society must

place a high priority on managing habitat. Human populations and economic activities will continue to expand, placing ever-increasing demands

on the environment and the habitats it contains.

Gaps in the relevant scientific information must

be filled, and the information communicated, so

that decisionmakers can be appropriately informed

as policy is developed and implemented. The National Marine Fisheries Service has developed the

Our Living Oceans series of reports to contribute

to these vital processes.

Above: Salt marsh, an important habitat for fish species.

Opposite page: Kelp forest,

providing habitat for many

species.

© OceansArt.us
3

INTRODUCTION

SCOPE AND HABITAT USE

HABITAT STATUS AND TRENDS

INFORMATION QUALITY AND RESEARCH NEEDS

ISSUES AFFECTING HABITAT

CONCLUSIONS

REFERENCES
4

NOAA

Cordell Bank National Marine Sanctuary

Top: Yellowtail rockfish swim near heavily encrusted rock

pinnacles in Cordell Bank National Marine Sanctuary off

California.

Middle: Coral at Ailuk Atoll, in the Marshall Islands.

Bottom: A small Dungeness crab in eelgrass at the Padilla

Bay National Estuarine Research Reserve off Washington.

NOAA DOI Office of Insular Affairs

Many of our Nation’s

living marine resources

depend on living habitats
5

INTRODUCTION

In 2006, commercial and recreational fisheries supported over 2 million jobs and contributed

over $73 billion to the United States gross national

product, making our Nation one of the largest

seafood-producing countries in the world. Until

quite recently, most people considered marine fishery resources to be abundant and inexhaustible.

Overfishing and natural environmental changes,

and habitat loss and degradation, including poor

water quality, have put increasing pressures on

coastal, anadromous, and oceanic resources. River,

lake, estuary, coast, and deep ocean habitats provide essential services such as food, shelter, and

space for reproduction and growth for many species, including fish, shellfish, crustaceans, birds,

marine mammals, and sea turtles. Habitat damage and loss threatens the sustainability of the

Nation’s fisheries and protected resources. It also

makes coastal areas much more vulnerable to hurricanes and coastal storms.

This abridged report provides an overview of

the first national summary of the status and trends

of the habitats used by the living marine resources

under the purview of NOAA’s National Marine

Fisheries Service (NMFS)1. The report is part of

the Our Living Oceans (OLO) series, joining OLO

Living Marine Resources and OLO Economics. For

the first time, there are comprehensive published

reviews of the Nation’s living marine resources, the

habitats they use, and the economic vitality and

value of the industries that depend on them. Appropriate information also is included in the full

OLO Habitat report on nearshore species managed by the states or regional state fisheries commissions.

The habitats addressed range from inland

streams used for spawning by anadromous species

(species that spawn in fresh water, but grow to

maturity in salt water, such as salmon) to the entire U.S. Exclusive Economic Zone (EEZ)

bounded by the 200 n.mi. (370 km) limit, and

beyond. This report provides a conceptual framework and a baseline for future updates on habitat,

identifies the shortcomings in relevant information, and describes how these shortcomings can

be addressed through additional research.

Importance of Habitat

Habitat can be defined as the places where organisms live, including areas used in every life stage

and activity. For fish, habitat supports spawning,

feeding, growth, and shelter from predators.

Clearly habitat is essential for maintaining healthy

stocks of living marine resources.

Habitat is structured by both biotic (living)

and abiotic (non-living) elements. Geological features are key abiotic elements. Examples include

intertidal rocks, subtidal or deep-sea sediment, and

seamounts that rise steeply from the abyssal plain.

Water itself is a critical abiotic component of habitat. Attributes of sea water, such as salinity (determined by the mixing of fresh and sea waters), play

a major role in defining the habitat of estuarine

species. Farther offshore, ocean frontal zones, where

distinct bodies of water meet, provide food-rich

habitat for large pelagic predators, such as tunas.

The biotic components of habitat consist of living

or dead organisms. Some biotic components are of

plant origin, such as the grasses that grow in salt

marshes, submerged aquatic vegetation (e.g. eelgrass), and kelp beds. Others are of animal origin,

such as oyster bars and coral reefs. Some marine

species can opportunistically occupy man-made

habitats, including oil rigs, pier pilings, and bridges,

which attract encrusting invertebrates and fish.

Ecosystem Approaches to Management

In recent years, momentum has been building for a shift in fisheries management away from

the traditional single-species approach and towards

ecosystem approaches (NRC, 1999). In its basic

form, the single-species approach relies on an assumption that abundance of a target stock is affected only by factors such as the abundance of its

spawning adults, natural mortality and mortality

caused by fishing, and the recruitment of juveniles to its population. This enables a mathematical modelling approach to stock assessment. Because other factors are not considered, there is an

Jim Raymont, Florida Keys NMS

1See http://spo.nwr.noaa.gov/TM75.pdf for the full report.

Yellowtail snapper, a shallow-water reef fish included

in the Fishery Management

Plan (FMP) for the South

Atlantic Snapper-Grouper

Fishery, the FMP for Reef

Fish Resources of the Gulf of

Mexico, and the FMP for the

Shallow-water Reef Fish

Fishery of Puerto Rico and

the U.S. Virgin Islands, is

shown here in the Florida

Keys National Marine Sanctuary.
6

implicit assumption that the stock exists in isolation from the ecosystem in which it resides.

Ecosystem approaches to management are still

evolving, but generally embody a more holistic

philosophy. They include a broader focus on ecological relationships and processes, and interactions

with humans. They also include a broader consideration of management tradeoffs by placing the

management of natural resources, such as fish

stocks and their habitats, into a broader context

of societal priorities, such as ecosystem services

(e.g. improved water quality), scenery, employment, and economic activity.

Operationally, implementation of ecosystem

approaches to management requires that the essential ecosystem components and processes be

conserved. Habitat, as a functioning element of

ecosystems, is clearly a major consideration in this

new and evolving philosophy of management.

NMFS Responsibilities for Habitat

Several Federal agencies and state and local

governments participate in decisions involving

conservation and protection of aquatic habitats.

The major Federal agencies outside of NOAA include the U.S. Army Corps of Engineers, the Environmental Protection Agency, the Department

of Agriculture, the Federal Energy Regulatory

Commission, and the Department of the Interior.

Notable U.S. habitat protection legislation includes the Clean Water Act, which aims to prevent destruction of aquatic ecosystems; the National Environmental Policy Act, which requires

Federal agencies to analyze the potential effects of

any proposed Federal action that would significantly affect the environment; and the Federal

Power Act, which provides authority to NMFS to

recommend hydropower license conditions.

The most important laws governing many of

the activities of NMFS pertinent to habitat are

the Magnuson-Stevens Fishery Conservation and

Management Act (MSFCMA) and two laws on

protected species: the Endangered Species Act

(ESA) and the Marine Mammal Protection Act

(MMPA).

The MSFCMA, which was originally enacted

as the Fishery Conservation and Management Act

in 1976, amended through the Sustainable Fisheries Act in 1996, and most recently reauthorized

in 2007, is the primary legislation governing marine fisheries. The original act established eight

regional Fishery Management Councils to manage fisheries in the EEZ under Fishery Management Plans (FMPs). Essential Fish Habitat (EFH)

provisions were added with the Sustainable Fisheries Act in 1996. The recent reauthorization

through the 2006 Magnuson-Stevens Reauthorization Act (MSRA), which was signed into law in

January 2007, did not include any changes affecting EFH regulations or guidance. However, it authorized the Community-based Restoration Program for Fishery and Coastal Habitats, established

the Deep Sea Coral Research and Technology Program, and directed FMPs to designate zones to

protect deep-sea corals from damage or loss due

to fishery gear interactions.

To implement the EFH provisions, NMFS and

the Councils are required to undertake the following three activities:

Designate EFH—describe and identify EFH for

each life stage of the species included in their

FMPs.

Minimize to the extent practicable the adverse

effects of fishing on EFH—Fishing impacts to

EFH must be assessed and minimized to the extent practicable, taking into special consideration

Habitat Areas of Particular Concern (HAPC),

The definition of Essential Fish Habitat stresses the importance of having ample, healthy habitat available, especially

when different habitats are required for each stage of life:

“. . . those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity” [MagnusonStevens Act, 16 U.S.C. 1802(10)].
7

which are habitats that are especially sensitive. This

may lead to fishing gear restrictions and time/area

closures.

Consult on potential impacts to EFH—Comments must be provided on activities proposed by

Federal action agencies (e.g. U.S. Army Corps of

Engineers) that may adversely impact areas designated as EFH.

The ESA and the MMPA define the protected

species mandates of NMFS. Under the ESA,

NMFS is responsible for protecting marine species that are threatened with, or in danger of, extinction. Fish, invertebrates, sea turtles (when in

the marine environment), most marine mammals

(cetaceans [whales, dolphins, and porpoises] and

pinnipeds [seals and sea lions]), and marine plants

are included. Critical habitat that contains physical or biological features essential for conservation

must be identified for every species listed under

the ESA, and NMFS issues Biological Opinions

for Federal actions that may impact the critical

habitat of listed species. Under the MMPA, NMFS

is responsible for protecting all species of cetaceans

and pinnipeds, regardless of their status under the

ESA. When human-related impacts are identified

that may cause declines or impede recovery of

marine mammal stocks, NMFS is responsible for

developing and implementing measures to alleviate these impacts on rookeries, mating grounds,

feeding grounds, migratory routes, or other ecologically significant areas.

SCOPE AND HABITAT USE

For this report, the United States was divided

into five regions: Northeast, Southeast, Pacific

Coast, Alaska, and Pacific Islands (Figure 1). To

develop the data for the report, habitat specialists

reviewed available data for each of the Federally

managed or protected species in their region and

classified them as to how frequently each species

uses four types of habitat: freshwater, estuarine,

Alaska Region

Southeast 

RegionPuerto Rico 

and U.S. 

Virgin Islands

Northeast 

Region

Pacific Coast Region

Pacific Island Region Midway Island

Hawaii

Palmyra Atoll and Kingman Reef

Jarvis Island

Howland and Baker Islands

Johnston Island

American Samoa

Wake Island

Northern Mariana Islands

Guam

Figure 1

Living marine resources in

the Exclusive Economic

Zone (EEZ) of the United

States are managed by

NMFS. The EEZ is divided

into five regions in this report.
8

shallow marine (<200 m [<656 ft] depths), and

oceanic (>200 m depths). The specialists also determined the relative quality of the available information for each of the Fishery Management

Plans (FMPs) or species groups,1 using the information levels for EFH, as defined in the

MSFCMA. These levels are: Level 1 (distribution),

Level 2 (habitat-related density), Level 3 (habitatrelated growth, reproduction, and/or survival by

life stage), and Level 4 (habitat-specific production). This report also uses an additional level of

information quality, Level 0 (complete lack of scientifically credible data on habitat use). Although

not mandated in the ESA or MMPA, these same

levels were used to evaluate the quality of available information for protected species. The methods are described in greater detail in the complete

OLO Habitat report.

Figure 2 shows the percentage of each region’s

FMPs and species groups that use each of the four

habitat categories (FMPs can cover a single species or multiple species). Shallow marine habitats

are used by over 95% of Federally managed fishery species in all regions, followed by oceanic habitats, which are used by over 75% of Federally

managed fishery species and species groups. All

regions also exhibit a high degree of estuarine usage, with the exception of the Pacific Islands, which

have relatively little estuarine habitat. There are

relatively few FMPs (and none in the Pacific Islands) that include any species, such as anadromous salmon, that use freshwater areas.

Figure 3 shows the percentages by region of

habitat usage by three distinct groups: cetaceans

(whales, dolphins, and porpoises), pinnipeds (sea

lions and seals), and sea turtles. As the figure shows,

these animals use shallow marine and oceanic habitats in every region. The three groups also use estuarine habitats to some degree in every region

except the Pacific Islands Region, which has relatively little estuarine habitat. Fresh water is the

habitat least used by the Nation’s cetaceans, pinFigure 3 nipeds, and sea turtles, as only pinnipeds in the

Percentage of protected

species groups (cetaceans,

pinnipeds, and sea turtles)

that use each habitat type

by each region.

Percent 

0 

20 

40 

60 

80 

100 

Northeast Southeast Pacific Coast Alaska Pacific Island 

Region 

F E S O F E S O F E S O F E S O F E S O 

F = Freshwater E = Estuarine S = Shallow marine O = Oceanic

Figure 2

Percentage of FMPs and

species groups that use

each habitat type by region.

0 

20 

40 

60 

80 

100 

Percent 

Northeast Southeast Pacific Coast Alaska Pacific Island 

Region 

F E S O F E S O F E S O F E S O F E S O 

F = Freshwater E = Estuarine S = Shallow marine O = Oceanic 

1For this analysis, four FMPs in the Southeast Region that

cover many species with different habitat associations were

divided into a total of 18 species groups. See the complete

OLO Habitat report for a detailed discussion.
9

Pacific Coast and Alaska Regions, and one cetacean (the beluga whale), occasionally use Alaskan

freshwater habitats.

HABITAT STATUS AND TRENDS

Geospatial data on the amount and condition

of the habitats used by the species managed by

NMFS are collected and held by many different

organizations, and for many different purposes.

Scientific standards and classification systems vary

widely. Hence, a quantitative analysis is simply not

feasible. However, it is clear that habitat impacts

occur where human activities alter the environment. Consequently, habitats in proximity to high

human population densities tend to be subjected

to the highest degree of stress. The general trend

is that habitat loss and degradation are highest in

freshwater and estuarine habitats, where the impacts of development and pollution are most direct, and lowest in shallow marine and oceanic

habitats, where fewer human activities occur.

The quantity and quality of the water in many

freshwater habitats have been declining for over a

century. Farming, industrialization, residential expansion, and flood control have reduced the flow

of fresh water, changed the timing and severity of

flood events, and increased the quantity of nutrients and contaminants draining from upland habitats (Heinz Center, 2002). For example, 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

(PSMFC, 2006). In the last 10 years, efforts have

been made to restore access, but many areas, such

as those above Grand Coulee Dam, remain inaccessible to Pacific salmon. Diversion of fresh water can significantly modify reproductive patterns

and success for anadromous fish such as salmon.

Reduced freshwater inflow and flushing in the bays

and estuaries that are downstream results in

changes to salinity distributions, which greatly affect the habitats of estuarine species.

Estuarine habitat also has been dramatically

impacted by human activities. For example, within

Puget Sound and California, more than 70% of

estuarine wetlands have been lost due to factors

such as pollution, diking, and filling (Emmett et

al., 2000), though much of that occurred long ago,

and efforts are underway to protect and restore

these habitats in many areas. The loss of submerged

vegetation continues in many estuaries, often due

to an excess of suspended sediment associated with

poor land-use practices, as well as algal blooms

stimulated by excess nutrients, which block light

penetration. Beds of submerged aquatic vegetation are almost completely absent from Delaware

Bay and nearby coastal bays (Bricker et al., 2007).

Chesapeake Bay submerged aquatic vegetation has

shown a rebound from extremely low levels in

1984 due to some improvements in water quality.

Although the Bay’s underwater grasses covered almost 26,300 hectares (65,000 acres) in 2007,

nearly double the 1984 levels, this is still only 35%

of the way towards the 2010 restoration goal of

75,000 hectares (185,000 acres) (Chesapeake Bay

Program, 2008).

The continued loss of wetland habitats in

coastal areas is a particular concern. These wetlands comprise about one-third of all the wetlands

in the continental United States, and are important to diadromous fish and to maintaining the

overall health of the estuaries. Coastal wetlands,

particularly coastal freshwater wetlands, continue

to be lost at a disproportionately high rate, compared to inland wetlands. Estimates for 1998 to

2004 show that coastal wetlands continue to be

lost at a rate of tens of thousands of acres per year

1:20,000

0 1,250 2,500 3,750 5,000 625

Meters

Legend

Date High Tide Acres

295

306

289

278

267

October 2002

October 2003

October 2004

Septem ber 2005

October 2006

Septem ber 2008 188

LA TX

MS

Accretion (land growth): approximately 57 acres

Erosion (land loss): approximately 165 acres

East Timbalier Island, off the

southeastern coast of Louisiana, is shrinking and being

pushed shoreward due to

the combined effects of sealevel rise, land subsidence

(sinking), and Hurricanes

Rita and Katrina. These

forces cause the sediments

from the seaward margins

of the island to erode. Some

of those materials are redeposited on the landward

side, and some are carried

away. The island lost over

35% of its above-high-tide

area between October 2002

and September 2008.

NOAA and USGS
1 0

(Zedler et al., 2001; Dahl, 2006). This loss is greatest in freshwater non-tidal forested wetlands on

the coast. Coastal watersheds experienced a net

loss of wetlands of around 23,877 hectares (59,000

acres) per year between 1998 and 2004. Estuarine

coastal wetlands declined at an annual average rate

of 2,240 hectares (5,540 acres) per year, with valuable estuarine salt marshes experiencing the steepest declines (Stedman and Dahl, 2008). Most of

that loss was in coastal Louisiana.

Much of the loss of wetlands occurred in the

distant past. For example, between 1780 and 1980,

it is estimated that California lost over 90% of its

wetlands, Connecticut lost 74%, Maryland lost

73%, and the majority of the other coastal states

lost at least 50% or more. With the advent of Federal and state laws requiring a permit for many

activities that destroy wetlands, wetland losses have

slowed in recent decades. However, with more than

half of the Nation’s population living within 50

miles of the coast, development pressure in coastal

areas continues to result in wetland loss.

Shallow marine and oceanic habitats generally

have good water quality, and relatively little habitat has been lost to human activities. Nevertheless, there are significant problems, such as the Gulf

of Mexico “dead zone,” where the water underlying the Mississippi River plume may contain little

or no oxygen during the summer (Rabalais et al.,

2002), and the impacts of some fishing gear, particularly bottom trawls, on seafloor habitats. There

are additional unquantifiable but generally negative effects from plastics and other debris in the

sea, oil spills and slicks, and discarded or lost

(ghost) fishing gear. Harmful algal blooms and

other toxin-producing algae, which can render seafood unfit for consumption by marine animals,

people, or pets, are a recurring problem in some

areas. At least some portion of this problem may

be caused by increased nutrient inflows, and the

problem could increase if ocean temperatures

warm as projected in climate change scenarios.

Many facets of climate change (warming, sea-level

rise, sea-ice loss, oceanic acidification, etc.) will

further stress habitats and could exacerbate the

effects described here.

INFORMATION QUALITY

AND RESEARCH NEEDS

In providing scientific advice on habitat-related

issues to resource managers and officials responsible for living marine resources, information is

needed on how species use habitat, where habitat

exists, its quantity and condition, the best practices to conserve it, and how marine communities, and, ultimately, sustainable fishery yields, depend on the amount and condition of available

habitat. Species in all habitats, including the open

ocean, are vulnerable to inappropriate human actions when their habitat requirements, availability, and dynamics are not known.

The quality of habitat-related information has

a major effect on the quality of decisions that are

based on it. An assessment of the quality of habitat information was done to identify gaps in the

available information and to identify research

needed to fill those gaps.

Information Quality

At the national level, habitat information for

most Federally managed FMPs or species groups

(as a whole or by life stage) primarily consists of

distribution (Level 1) and habitat-related density

(Level 2) information (Figure 4). Less information is available for habitat-related growth, reproMary Hollinger, NODC, NOAA

Reeds and a narrow channel

at low tide in a marsh on the

Patuxent River.
1 1

duction, and/or survival by life stage (Level 3), and

habitat-specific production (Level 4) information

is rare. Approximately 11% of the information is

Level 0, indicating a complete lack of data on habitat use for one or more species (or life stages) within

the given FMP or species group. However, the

species and species groups with unknown habitat

use generally constitute a relatively minor portion

of the commercial and recreational catch.

Information on habitat-specific productivity

(Level 4) is the highest and most quantitative level

of information for identifying EFH, and provides

the most definitive information for understanding relationships between species and their habitats. Such information is necessary for quantifying the contributions of specific habitats to the

production of a species. Level 4 information is

generally not available for even the most valuable

species. The main exceptions include Alaska

salmon in fresh water and a species of seaweed,

Atlantic Sargassum, in shallow marine and oceanic

habitats.

Figure 5 depicts the levels of habitat-use information available for the protected species groups

(cetaceans, pinnipeds, and sea turtles) at the national level. Approximately 15% of the information is Level 0, indicating a lack of habitat-use data

for some species in particular habitats. Data gaps

exist on habitat for particular life stages of various

sea turtle species in shallow marine and oceanic

habitats of the Northeast, Southeast, and Alaska

Regions, as well as in estuarine habitats of the

Northeast and Southeast Regions. There is a complete absence of data for some cetaceans in shallow marine and oceanic habitats in the Northeast,

Southeast, and Pacific Islands Regions. Of all the

habitat-use information, distribution information

(Level 1) accounts for approximately 45%, habitat-related density information (Level 2) accounts

for approximately 31%, and habitat-specific

growth, reproduction, or survival information

(Level 3) accounts for 10%. This general pattern

is consistent with the pattern of information levels for fishery species. However, no habitat-specific productivity information (Level 4) exists for

any of the Nation’s cetaceans, pinnipeds, or sea

turtles.

Figure 5

Habitat use information levels available for protected

species groups (cetaceans,

pinnipeds, and sea turtles),

all regions combined.

0 

20 

40 

60 

80 

100 

Level 0 Level 1 Level 2 Level 3 Level 4 

Percent

Information level 

Figure 4

Habitat use information levels available for Fishery

Management Plans and species groups, all regions

combined.

0 

20 

40 

60 

80 

100 

Level 0 Level 1 Level 2 Level 3 Level 4 

Percent 

Information level 

Level 0 = No credible data on distribution

or habitat use.

Level 1 = Distribution data for some or all

portions of the geographic

range.

Level 2 = Habitat-related density data.

Level 3 = Data on growth, reproduction,

or survival rates within habitats.

Level 4 = Data on production rates by

habitat.
1 2

Research Needed

The fundamental goal for NMFS’s habitat research is to provide managers with the information they need to optimize the benefits society

derives from our living marine resources while

maintaining long-term ecological sustainability.

Understanding species–habitat relationships is an

important component of the information required

for implementing ecosystem-based approaches to

management, including setting fishery targets,

ensuring recovery of species of conservation concern, protecting and restoring habitat, and maintaining ecosystem functions. There are many factors to consider in setting habitat-research priorities, including the economic value of harvested

species, conservation concerns for overfished or

protected species, the roles of species in the ecosystems they occupy, the degree of dependence of

species on their habitats, and the vulnerability of

those habitats to human-caused or natural disturbance, including climate change.

Addressing the fundamental goal identified

above requires obtaining new information through

research, as well as making better use of the information that already exists. From the management

perspective, the highest priorities for habitat research should be the life stages most sensitive to

habitat concerns or that play a major role in determining population dynamics, and the habitats

most vulnerable to disturbance. For species of

minimal economic, conservation, or ecological

importance, information on presence/absence or

density by habitat type may suffice. For the most

important or sensitive species and habitats, productivity data by habitat type will provide the most

comprehensive information to scientists and the

managers they advise.

Key research needs are summarized in Table

1. Even for the most-studied fishery species, which

have been the subject of intensive research for

many years, important questions related to fish–

habitat linkages remain unanswered. These include: seasonal habitat usage by life stage, relationships between habitat alteration and fish survival

and production, lethal and sublethal effects of pollutants, and effectiveness of restoration techniques.

Table 1

Key habitat research needs identified by NMFS scientists.

Determine critical habitat requirements for each

species and life stage.

Conduct life history studies (including studies of

age, growth, maturity, and fecundity) and relation

to environment for all managed species,

particularly for the early life stages.

Determine impacts of natural and human-caused

habitat variability.

Characterize and describe seafloor and openocean habitats and associated fish assemblages

on spatial scales relevant to fishery management

and habitat protection.

Delineate and map important habitats including

coastal shorelines, estuaries, salt marsh wetlands,

anadromous streams, riparian zones, submerged

aquatic vegetation (e.g. eelgrass), deepwater

corals, pinnacles, seamounts, and fishing grounds

on the Continental Shelf and Slope.

Determine effects of fishing gear on all species

and their habitats, and develop methods to reduce

damaging practices.

Develop and implement advanced methods for

research and management, including remote

sensing for oceanography and stock assessment,

and the use of marine protected areas.

Expand research and monitoring of habitat

condition.

Develop methods to protect and restore habitat.

Determine societal and economic benefits of

conserving and restoring habitat.

Research needs

Above: Eelgrass meadows

in the Waquoit Bay National

Estuarine Research Reserve,

Massachusetts.

R. Crawford, NOAA National Estuarine Research Reserve Collection

Below right: Wetlands and

tidal streams in the Ashe Island area of the ACE Basin

National Estuarine Reserve,

South Carolina.

NOAA
1 3

Many of the same research needs exist for

marine mammals and sea turtles as for fishery resources. A primary research need is to characterize habitats for cetaceans, and to better understand

movement patterns and local abundances. There

are recent and ongoing efforts to model cetaceanhabitat occurrence using oceanographic data, but

more detailed studies are needed to gain a better

understanding of important habitats and their variability. For endangered or threatened sea turtles,

the primary need is to determine habitat use during migration and while foraging (for example,

through tagging studies), and also to determine

abundance and trends at key forage areas and nesting beaches. This knowledge will enable mitigation of impacts from commercial fisheries and

other causes.

There are important research needs in the area

of habitat economics. It is necessary to inventory

and review the scattered existing information on

the economic values of habitat types, so that gaps

in our knowledge regarding different regions and

at different scales can be identified and addressed.

To support managers who evaluate proposed actions that may affect habitat, research is needed to

quantify the full range of potential costs and benefits to all sectors of society. Bioeconomic models

are needed that quantify cumulative effects of habitat degradation and loss, as well as the economic

consequences from beneficial uses, such as habitat restoration using dredged materials.

ISSUES AFFECTING HABITAT

As the U.S. population continues to grow,

there is increasing pressure on the environment to

provide humans with food, income, recreation,

and other resources (Heinz Center, 2002). This is

especially evident in coastal areas, where human

population growth is about five times faster than

in inland areas. Human use of aquatic habitats will

of course affect those habitats, and society faces

many choices, including how to responsibly manage growth, development, and resource use. To do

this wisely, society and decisionmakers must understand the consequences of their decisions, including the potential for habitat impacts. In situations where habitat impacts cannot be avoided,

decisionmakers must consider ways to reduce or

mitigate impacts and to restore damaged habitats.

Although the issues affecting U.S. living marine resource habitats vary throughout the country, many issues are widespread, even if the impacts are manifested differently in different regions.

Certain issues are important in all aquatic habitats, while others have greater impacts within a

certain habitat type. The following section presents information on seven of the most important

issues on a national scale:

• Pollution and water quality;

• Alteration and degradation of rivers and

migratory pathways;

• Fragmentation and loss of estuarine and

shallow marine habitats;

• Fishing effects on habitat;

• Climate variability and change;

• Invasive species and marine debris; and

• Vessel traffic and noise.

Information is also provided on ways to reduce or

mitigate impacts, and on progress that has been

made.

Mangrove habitat is essential to many juvenile fish

species in the subtropical

Atlantic and Gulf of Mexico

coastal waters.

NOAA
1 4

Upper photo: Cleaning up

oil from the 1989 Exxon

Valdez spill. Approximately

2,080 km (1,300 mi) of shoreline in the region of Prince

William Sound, Alaska, was

impacted. About 320 km

(200 mi) was moderately or

heavily oiled, especially intertidal habitats. Although

massive mortalities resulted, many of the living

marine resources have recovered. Nonetheless, residual oil remains in some

habitats, with chronic impacts on the species that

spawn or forage in the affected areas.

Lower photo: Close up of

Exxon Valdez oil on the

beach.

POLLUTION AND WATER QUALITY

ISSUE:

POLLUTION AND WATER QUALITY

Water itself is habitat. Reduced water quality

results from point sources, which release harmful

substances into the water from a discrete source,

from spills, from non-point sources, which are

more diffuse and widespread, and from atmospheric deposition.

The U.S. Environmental Protection Agency

(EPA, 2008a) rated the overall quality of the

Nation’s coastal waters as good to fair and improving, with the best ratings in Alaskan and Hawaiian waters. Sediment quality was rated good to

fair overall, also with the best ratings in Alaska

and Hawaii, but with poor ratings in the Gulf of

Mexico and Puerto Rico.

Habitat Impacts

Excess nutrients can come from point sources

(e.g. sewage treatment plants), from non-point

sources (e.g. runoff from farms and suburbs), and

from small particles deposited from the atmosphere. Although not directly toxic, their effects

are pervasive, especially in estuaries and coastal waters. They overstimulate algal growth, leading to

eutrophication (Rabalais et al., 2002; Bricker et

al., 2007). Eutrophic waters contain reduced oxygen, are typically highly turbid (reducing the

growth of submerged aquatic vegetation), or may

be impacted by harmful algal blooms that can be

toxic to fish, or even to humans.

Stormwater runoff contains many harmful

materials. The sediments washed from cities, suburbs, construction sites, and farm fields can

smother marine plants and also carry contaminants

such as pesticides, oil and grease, and pathogens.

Particulates from the atmosphere can be deposited as dust, or carried in precipitation. This is

becoming recognized as a significant source of

nutrients and certain contaminants, such as the

heavy metal mercury.

Toxic chemicals, such as heavy metals, petroleum products, and pesticides, can be lethal in high

concentrations. Even at sub-lethal concentrations,

toxic chemicals can accumulate in the environment, often in sediments, where they can remain

for a very long time. For example, the insecticide

DDT was banned in the United States in 1972,

but it is still readily found in the sediments of many

of our Nation’s waterways and in the bodies of

living marine resources.

Impacts to Living Marine Resources

Poor water quality degrades ecosystems, lowering the productivity of many fishery and protected species. According to a recent NOAA report (Figure 6; Bricker et al., 2007), approximately

two-thirds of the estuaries along the coasts of the

continental United States exhibited at least moderate symptoms of eutrophication in 2004. Oxygen

levels that are too low cannot support marine life,

and the loss of submerged aquatic vegetation reduces important habitat and food for many estuarine and coastal species. Toxic algal blooms have

been implicated in the mortality of fish and marine mammals along coastal areas and are likely

having impacts throughout the food chain. Significant portions of U.S. fishing areas are closed

each year to protect the public from sewage contamination and potentially dangerous concentrations of algal toxins in shellfish.

Chemical spills can cause acute mortalities of

marine mammals, seabirds, fish, and invertebrates.

However, chronic impacts are often a greater concern. Many substances, including metals, pesticides,

and other organic compounds, can bioaccumulate, increasing in concentration in the tissues of

animals that feed on contaminated food sources,

increasing mortality and reducing reproduction.

Solutions

Progress has been made to reduce water quality impacts, particularly from point sources. Technology exists to monitor and reduce point sources

of pollution, and the Clean Water Act has regulated point-source discharges since 1972. Regulations exist to ensure proper cleanup of contaminants after an oil or chemical spill as well. Enforcement of such laws has reduced the prevalence

Exxon Valdez Oil Spill Trustee Council ORR, NOS, NOAA
1 5

POLLUTION AND WATER QUALITY

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Symptoms worsened since 1999 assessment. 

Symptoms improved since 1999 assessment. 

No change in symptoms since 1999 assessment. 

Insufficient data to show trend.

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High: symptoms occur periodically or persistently and/or over an extensive area.

Moderate high: symptoms occur less regularly and/or over a medium to extensive area.

Moderate: symptoms occur less regularly and/or over a medium area.

Moderate low: symptoms occur episodically and/or over a small to medium area.

Low: few symptoms occur at more than minimal levels.

Unknown: Insufficient data for analysis.

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Overall eutrophic condition (OEC) Change in eutrophic condition since 1999 assessment

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and impacts of point-source pollution on water

quality and improved the Nation’s waterways, but

additional progress is needed.

Less progress has been made at controlling

non-point sources of pollution (Heinz Center,

2002; Chesapeake Bay Program, 2008), because

it was more recently recognized as a problem and

is much more diffuse than point-source pollution.

Although non-point source pollution is difficult

to control, sections of the Clean Water Act require

jurisdictions to reduce surface runoff to the “maximum extent practicable.” Individuals and citizen

groups can reduce non-point pollution through

awareness and environmentally responsible actions

(e.g. proper disposal of household chemicals, maintenance of septic systems and cars). Improved landuse practices can reduce run-off from urban and

agricultural landscapes, as well as reduce the concentrations of contaminants in the water that does

run off. Spills can be prevented (e.g. by requiring

enhanced safety practices for industrial facilities

and shipping), and the clean-up of spills can be

expedited.

Bricker et al. , 2007

Figure 6

Eutrophic conditions in U.S.

coastal waters in 2004, and

change since 1999 (Bricker et

al., 2007).

Josh Harper, Texas Department of Parks and Wildlife

NOAA

Left: NOAA ship surveys of

water quality show low oxygen areas in the Gulf of

Mexico “dead zone” as reds

and oranges.

Right: Gulf menhaden killed

by hypoxia in Matagorda

Bay, Texas.
1 6

ISSUE:

ALTERATION AND DEGRADATION OF

RIVERS AND MIGRATORY PATHWAYS

Many factors affect river habitats, such as urbanization, agriculture, timber harvest, and mining. Of these activities, dams and other water-control structures have the greatest overall impacts.

There are thousands of these structures in U.S.

rivers. For example, the Columbia River and its

main tributaries contain over 250 reservoirs and

150 hydroelectric projects, including 18 mainstem

dams.

Habitat Impacts

Dams fragment river habitats and present impediments to catadromous fishes such as eels

(which spawn in the ocean and grow to maturity

in fresh water) and anadromous fishes such as

salmon, sturgeon, striped bass, shad, and river

herring (Roni, 2005; NMFS, 2008). Dams also

change upstream habitat by creating reservoirs that

slow water velocities and alter temperatures. Reduced freshwater flows resulting from water removals for domestic and commercial use can affect river and downstream estuarine habitats as

well. Altering natural flows and the processes associated with flow rates (such as nutrient and sediment transport) impact in-stream habitats, shoreline riparian habitats, and prey bases. Water quality may also be reduced from water withdrawals:

temperature, salinity, and concentrations of toxic

chemicals all increase as water volumes shrink;

dissolved oxygen decreases; and pathogens may be

introduced.

Changes to stream beds and banks and streamside vegetation can have major impacts on adjacent aquatic habitats. Hydrologic characteristics

such as temperature and dissolved oxygen can be

altered, and habitat complexity can be reduced by

lowering the availability of large woody debris.

Changing flow and channel structure, increasing

stream bank instability and erosion, and altering

nutrient and prey sources also degrade riverine

habitat.

Impacts to Living Marine Resources

By blocking upstream access for migrating

species, dams greatly reduce the amount of habitat available for spawning, feeding, growth, and

migration. Adequate freshwater flow is critical to

all life stages, from eggs to spawning adults, so

reduced flow can have a negative effect on anadroTodd Bennett, NMFS

WASHINGTON 

IDAHO 

OREGON 

CANADA 

UNITED

MONTANA 

Snake River

Snake River

Salmon River

Clark Fork River

Columbia River

Deschutes River

Willamette

Columbia R.

Pacific Ocean

Owyhee River

Bend 

Boise 

Yakima 

Eugene 

Olympia 

Medford 

Spokane Seattle 

Richland Lewiston 

Missoula 

Portland 

Kalispell 

Pendleton 

Pocatello 

0 80 160 240 40 

Miles 

Map by StreamNet Project for

PSMFC, November 2006

Accessible Habitat 

Blocked Habitat 

Major City 

Major River 

Columbia Basin 

Left: Accessible and blocked

anadromous fish habitat in

the Columbia River basin.

On the Columbia River and

its main tributaries, over 250

reservoirs and 150 hydroelectric projects reduce access and use of a majority

of the 647,500 km2

 (250,000

mi2

) drainage basin (PSMFC,

2006).

Right: Spawning pink

salmon are holding in a pool

in Bacon Creek, Washington.

Note the clean gravel in the

riverbed that is clear of mud

and silt. This is a requirement of habitat suitable for

egg laying.

ALTERATION AND DEGRADATION OF RIVERS AND MIGRATORY PATHWAYS PSFMC, 2006
1 7

mous and catadromous fish populations. As an

example, a drought extending from 2001 through

2005 in the Klamath River basin of California and

Oregon, combined with above-average withdrawals for agricultural use during the drought, allowed

for the proliferation of endemic diseases, causing

large fish kills. As a result, the Klamath River Chinook salmon stock fell below conservation objectives. This triggered the declaration of a commercial fishery failure by the Secretary of Commerce

in 2006, which authorized a total of $60.4 million for distribution to eligible participants in the

West Coast salmon fishery (DOC, 2006).

Solutions

Healthy riparian corridors are important components of river ecosystems (Roni, 2005). The

most effective strategy is to conserve existing intact systems. However, human populations and

associated development are continuing to expand.

To reduce human impacts, activities such as urban development, mining, and timber harvest

should maintain a reasonable minimum distance

between streams and rivers and their operations.

Restoration activities, such as native vegetation replanting and the addition of large woody debris,

are currently improving river habitats for anadromous species. An example is the Chewuch River

in Washington State, where restoration efforts have

been successful at improving habitat for resident

and migratory species of fish, including several

threatened or endangered species.

Mitigation measures, such as fish ladders and

barging of migrating juvenile salmon, may be partially effective, but are in place only at some dams

(NMFS, 2008). Juvenile bypass systems to guide

out-migrating juveniles past the turbines have efficiencies as low as 30% for some species. Moreover, mitigation often targets salmon exclusively,

ignoring the impact of dams on other anadromous

and freshwater species.

In some instances, removal of a dam can reverse habitat damage and restore historical river

flows and fish migration routes. For example,

Sennebec Dam, built in 1916 on the St. George

River in Union, Maine, blocked passage to over

half the St. George watershed for Atlantic salmon,

alewife, shad, eel, and river herring. By the end of

the 20th century, this was the only remaining barrier in the watershed. Trout Unlimited, with substantial NOAA funding, removed the dam in 2002

and replaced it with a roughened fish ramp about

0.4 km (0.25 mi) upstream. This resulted in 27

km (17 mi) of available fish habitat on the St.

George River, while increasing safety below the

former hydropower dam, reducing maintenance

costs, and maintaining the recreational value of

Sennebec Pond. Success stories such as this are

propelling a movement in the United States to

remove obsolete dams and restore healthy river

habitats.

Although dam removal has proved successful

at restoring damaged river habitats, it is often not

a viable option due to competing river uses (including use of dams for flood control). There is

currently heated debate about whether four dams

on the Lower Snake River in eastern Washington

should be removed (see Columbia River Basin map

on previous page). Removal would restore 225 km

(140 mi) of habitat that historically supported 50%

of salmon returning to the Columbia River Basin,

but would also eliminate substantial social and economic benefits that result from irrigation, electricity, and river navigation services that the dams

provide.

The removal, with the help of

NOAA funding, of New

Hampshire’s West Henniker

Dam, 18 feet tall, opened 15

miles of riverine habitat in

the Contoocook River to migratory fishes such as Atlantic salmon and American eel.

ALTERATION AND DEGRADATION OF RIVERS AND MIGRATORY PATHWAYS

New Hampshire Department of Environmental Services/NOAA
1 8

ISSUE:

FRAGMENTATION AND LOSS

OF ESTUARINE AND SHALLOW

MARINE HABITAT

Habitat loss occurs when habitat is destroyed

or altered to the point that it can no longer provide the requisite ecological functions. Habitat

fragmentation occurs when natural or human activities cause a habitat to become separated into

isolated areas, disrupting migratory corridors, isolating local populations, and disrupting or preventing access to portions of habitat necessary for food,

growth, or reproduction.

Habitat Impacts

A wide range of human activities in coastal

watersheds causes habitat loss and fragmentation.

While the effects of individual projects may be

relatively modest, the scale of human activities in

the coastal zone is so great that there are substantial cumulative effects. Placing fill in wetlands or

other aquatic habitats for development is a significant factor. Over-water, shoreline protection,

and water-control structures can have serious impacts on local habitat, including removal of vegetation and natural substrates, and blocking the

sunlight needed by aquatic plants. Dredging removes bottom habitat and degrades water quality

through increased turbidity and siltation, release

of oxygen-consuming substances and contaminants, and alteration of physical habitat and hydrographic regimes. Disposal of dredged material

can have these same effects and can smother

benthic habitats. Additionally, predicted climaterelated sea level rise threatens shallow marine habitats such as mudflats and salt marshes.

Wetland loss is widely recognized as a significant environmental problem (Dahl, 2006). For example, the average annual loss of wetlands in Connecticut between 1880 and 1970 was about 28

hectares (70 acres) per year, leading to a 30% loss

of wetlands state-wide over this period. More than

70% of the estuarine wetlands have been lost or

degraded in the Pacific Northwest and California.

Since the 1930’s, Louisiana has lost from 38 to

108 km2

 (15 to 42 mi2) of wetlands per year due

to land subsidence, sea-level rise, and erosion from

tropical storms. Flood-control levees on the Mississippi River channel the river’s drainage directly

into the Gulf of Mexico. This prevents the annual

floods that previously deposited new sediments

and detritus on the adjacent wetlands and marshes.

Impacts to Living Marine Resources

The loss or fragmentation of habitat reduces

the ecological services that habitat provides. The

species most affected are those that depend on

habitats where humans are most active, i.e. habitats located in watersheds, estuaries, or near the

coast. As shown previously in Figures 2 and 3, the

great majority of the fishery and protected-species stocks that NOAA manages use estuarine and

shallow-marine habitats, with the percentage that

use freshwater habitats varying by region. Even species that spend most of their lives far out at sea,

such as some anadromous fishes, marine mammals,

and seabirds, depend on these heavily-impacted

habitats for certain key aspects of their life histories, such as spawning, larval or juvenile growth,

calving, or nesting. Also, state-managed stocks,

which occur primarily in state waters inside the 3-

mile limit, all depend on these habitats.

Solutions

Solutions to habitat loss and fragmentation include conserving and protecting existing habitat,

and restoring or enhancing lost, fragmented, or

Above: Impacted and eroded

marsh on Staten Island, New

York.

NOAA

FRAGMENTATION AND LOSS OF ESTUARINE AND SHALLOW MARINE HABITAT
1 9

degraded habitat to recover ecological function.

Creating or restoring habitat is usually much more

expensive and less effective than protecting habitat that already exists and is functioning. The science of creating and restoring habitats is relatively

new, so more research is needed to develop and

evaluate restoration methods.

Understanding the relationships between species and habitats, and knowing where habitat exists, are the first steps toward habitat protection

and conservation. Thus a key ingredient for conserving habitat is developing and providing information to resource managers and the public about

habitat status, function, and relationship to various species. An example is Chesapeake Bay, from

which most of the submerged aquatic vegetation,

an important habitat that supports key species such

as the blue crab, has been lost due to centuries of

poor land use practices and declining water quality. The public has supported extensive regional

efforts to improve water quality. There has been a

rebound from the low point of 1984, such that

vegetated areas have roughly doubled. However,

the total vegetated area only covers approximately

one-third of the 2010 restoration goal of 75,000

hectares (185,000 acres) (Chesapeake Bay Program, 2008).

One successful approach to prevent habitat loss

is to provide legal protection. More than 1,000

areas within U.S. waters are granted some level of

special protection by Federal or state governments.

However, only about 1% of the ocean within U.S.

jurisdiction qualifies as marine protected area, and

only about 10% of that carries the highest level of

protection, where fishing and other extractive activities are precluded.

NOAA and partners designated protected status to three significant areas of the U.S. EEZ in

20061

. Marine waters totaling 388,500 km2

(150,000 mi2) off the U.S. West Coast were designated as Essential Fish Habitat for commercially

valuable fish. The Aleutian Islands Habitat Conservation Area encompasses over 950,000 km2

(366,795 mi2), an area approximately the size of

Texas and Colorado combined. The Papahanaumokuakea Marine National Monument contains

nearly 362,600 km2 (140,000 mi2) of emergent

and submerged lands and waters of the Northwestern Hawaiian Islands, including over 13,200

km2

 (5,100 mi2) of coral reefs and over 7,000

marine species. It is home to almost the entire

population of endangered Hawaiian monk seals

and is the breeding ground for over 90% of the

Hawaiian green sea turtle population.

The task of conserving and protecting habitats goes well beyond the abilities and funding of

state and Federal agencies. Individual citizens and

their organizations at the local, regional, and national levels are the key to successful actions. It is

through education and consciousness raising that

many harmful actions can be avoided or corrected.

1

On 6 January 2009, President George W. Bush designated

three new National Monuments in the tropical western

Pacific, with a total area of over 505,000 km2 (over 195,000

mi2

) (White House, 2009). The largely uninhabited areas

contain pristine coral reefs, volcanic ecosystems, and the

Mariana Trench, which, at some 11,000 m (36,000 ft) depth,

is the deepest region in the oceans. Protections include bans

on fishing and shipping.

Both photos © Peter Bergstrom

Local groups of concerned

citizens can take an active

role in conserving and restoring habitat. Here, members of the Magothy River

Association are planting

seagrass in a small tributary

on the western shore of

Chesapeake Bay, which has

been heavily impacted by

development, declining water quality, and habitat loss.

FRAGMENTATION AND LOSS OF ESTUARINE AND SHALLOW MARINE HABITAT
2 0

ISSUE:

FISHING EFFECTS ON HABITAT

The impacts of fishing on habitat can be very

significant, potentially resulting in ecosystem shifts

that include altered species composition, changes

in trophic structure, and reduced biodiversity.

Because of these concerns, the Magnuson-Stevens

Reauthorization Act requires that fishery management councils assess fishing impacts to EFH and

minimize the impacts of fishing to the extent practicable. Congress was aware this could lead to fishing gear restrictions and time/area closures.

Habitat Impacts

The effects of fishing gear on habitat can be

direct and indirect, and act over both short- and

long-term scales (Barnes and Thomas, 2002). The

impacts resulting from both fixed (longlines,

gillnets, traps, and pots) and mobile (trawls and

dredges) gear depend on the spatial extent of operations, level of effort, type of gear, and the sensitivity of the particular habitat. Mobile fishing

gear is of particular concern and may have a greater

effect on a regional scale, but other fishing practices (such as traps and gill nets) may have a more

significant ecological effect in local areas, depending on the nature of the fishery and habitat. Most

studies of the effects of fishing on habitat have

only looked at local spatial scales, making it difficult to apply results to management efforts on an

ecosystem level.

In addition to impacts from fixed and mobile

types of gear, destructive fishing methods such as

the use of poison or explosives cause major damage to marine habitats. These methods are often

used in coral reef habitats, killing or breaking apart

the living substrates these reefs provide. Such practices are banned in the United States, but may still

occur in U.S. island territories.

Habitats vary in their sensitivity. Fauna that

live in habitats with a low level of natural disturbance are generally more vulnerable. Such habitats often have large, slow-growing structures like

deep corals, which are likely to take many years to

recover from the damage caused by mobile gear

(Lumsden et al., 2007). Habitats that normally

experience high levels of natural physical disturbance (e.g. high-energy sandy bottoms) tend to

be less vulnerable to the impacts of mobile gear

(Link et al., 2005).

Substrate at Northeast Peak

in Georges Bank, off the

Massachusetts coast, which

is subjected to fairly high

levels of natural physical

disturbance due to storms

and strong tidal currents.

Left: Gravel habitat heavily

impacted by mobile fishing

gear. Note that the gravel is

clean, and that sand shows

between the pebbles.

Middle: Recovering seafloor

community that has been

closed to trawling for 2.5

years. Note that there is

some cover by attached organisms, primarily sponges.

Right: Unfished gravel habitat on the Canadian side of

Georges Bank. Note the

nearly full cover provided by

attached organisms.

FISHING EFFECTS ON HABITAT

Page Valentine, USGS
2 1

Impacts to Living Marine Resources

The significance to fisheries productivity of

gear impacts on habitat is generally not well

known. The vulnerability of habitats to gear impacts may be greater when fishing is combined

with other habitat stressors. Short-term effects are

usually directly observable and measurable. While

the impacts may be immediate, it may take years

before the damage is repaired. Of the greatest concern are the impacts of trawling and dredging on

habitat complexity. By directly damaging or removing living, structure-building components of

habitat such as corals and burrowing species, repeated trawling and dredging can reduce productivity of benthic habitats and result in discernible

changes in benthic communities. Removal of reefbuilding species will cause large changes to the

species assemblages associated with the reef structure itself. For example, repeated dredging of oyster reefs reduces not only the oyster population,

but the populations of all the species that use them

for foraging or shelter.

The longer-term effects of fishing may be indirect and are more difficult to quantify. Fishing

operations in an area can cause changes that linger long after the often immediate and measurable reductions in the densities of both target and

non-target organisms. Excess removal of species

can disrupt ecological function and balance,

change habitats, and allow undesirable species to

increase in abundance. For example, in Jamaica,

removal of herbivorous fishes through over-harvest initiated a massive ecosystem shift from a

coral-dominated reef community to a less productive algae-dominated system.

Solutions

Although fishing can have substantial impacts

on aquatic habitats, there are a number of ways to

reduce those impacts. Prohibiting or limiting fishing through time/area closures, allowing time for

living habitats to regenerate, and restricting gear

have been successful in protecting critical or sensitive habitats. More limited measures can also have

profound impacts. The Aleutian Islands Habitat

Conservation Area, designated by NOAA in 2006,

has enforced several fishing closures in the Aleutian Islands and Gulf of Alaska to protect deep sea

corals and other fragile parts of the ecosystem (e.g.

rockfish habitat, seamounts) from bottom trawling. An area this large has a complex set of regulations intended to protect undisturbed or sensitive

habitat, while allowing economically valuable fishing to continue. For example, bottom trawling is

allowed in areas that have supported the highest

catches of groundfish in the past, and is prohibited in all other areas to protect relatively undisturbed habitats.

More research is needed to further reduce the

impacts of fishing gear on habitat. This includes

research to better understand the ability of habitats to sustain fishing impacts; research on habitat

restoration, especially for fragile biological habitats, such as corals; and research to develop less

damaging fishing gear.

FISHING EFFECTS ON HABITAT

Left: The deepwater coral

Lophilia in its natural state.

Right. A Lophilia coral reef

after bottom trawling.

© Both photos courtesty of Mareano, Institute of Marine Research, Norway
2 2

ISSUE:

CLIMATE VARIABILITY AND CHANGE

Natural climate variability can be seemingly

random from year to year, may operate over several years, such as the 2- to 7-year cycle of the El

Niño Southern Oscillation, over decades, such as

the North Atlantic Oscillation, or even over millennia, such as the ice ages. Some species and populations can adapt to climate change, while others

may virtually disappear or go extinct.

Superimposed on this natural variability is a

new threat from human-induced (or anthropogenic) global warming, widely believed to be

caused by emission of greenhouse gases, such as

carbon dioxide from burning fossil fuels. Warming of about 0.74°C (1.5°F) has been observed

over the last 100 years. The Intergovernmental

Panel on Climate Change (IPCC, 2007) projects

further global warming of 1.1–6.4°C (2.0–11.5°F)

by the year 2100. NOAA paleoclimatological data

show that the earth has not been as warm as the

projection’s lower bounds since the last interglacial period, 120,000 years ago (NOAA, 2006).

Habitat Impacts

Regional and local changes will differ from the

global averages discussed here, and some habitats

are more vulnerable to these changes.

Increases in ocean temperatures have been

widely detected. Predicted impacts include more

increases in water temperature, changes in ocean

currents, and increased intensity of tropical storms.

There have been major losses of polar ice in the

last few decades, although the Antarctic changes

are not uniform and tend to balance. Because of

thermal expansion of the oceans and ice melting,

global mean sea level has been rising at an average

rate of 1–2 mm (0.04–0.08 in) per year over the

past 100 years, significantly faster than the rate

averaged over the last several thousand years. The

projected increase in sea level by 2100 is anywhere

from 0.18 to 0.59 m (7.1–23.2 in).

Another effect of carbon dioxide emissions that

is only recently beginning to receive attention is

ocean acidification. Approximately 30–50% of

global anthropogenic carbon dioxide emissions

are absorbed by the world’s oceans, which is expected to increase surface ocean acidity by 0.14–

0.35 pH units over the next century. Depending

on emissions, the increase in ocean acidity over

the next few centuries is expected to exceed the

changes seen over the past few hundred million

years.

Impacts to Living Marine Resources

Some species will be negatively impacted under most scenarios for human-induced climate

change, while other species may benefit. Several

potential negative impacts from global warming

include accelerated loss of beaches and wetlands

due to sea level rise, loss of habitat for cold-water

and ice-dependent species, coral bleaching,

changes in ecosystem productivity, and seasonal

timing of physical and life-history events. Positive

impacts may include decreased winter mortalities

of some species and increased habitat availability

for some warm-water species.

Coral bleaching is a symptom of environmental stresses such as diseases, sedimentation, pollution, and increased temperature. In a bleaching

event, coral polyps expel the photosynthetic cells

of unicellular algae, called zooxanthellae, which

normally live symbiotically within their tissues and

provide nutrients and a characteristic color. The

Budd Christman, NOAA Corps

Above: A group of walrus

hauled out on sea ice in the

Bering Sea. As sea ice disappears due to climatic

warming, so too does the

ecosystem it supports and

the habitat it provides.

CLIMATE VARIABILITY AND CHANGE
2 3

remaining carbonate skeleton is light in color, and

looks as if it were bleached.

In the bleaching event shown in adjoining

photograph on the next page, over 89% of the

live coral was bleached, including brain coral (in

the foreground) and mountainous star coral (large

colonies in the distance), which are the dominant

reef builders in the western Atlantic. Certain fast

growing taxa (lettuce coral and file coral) experienced extensive mortality, while long-lived species

like those shown suffered partial mortality affecting up to 40% of their surface. From the fisheries

perspective, loss of the living coral means that the

habitat it provides for coral reef-dwelling fish will

also be lost.

Ocean acidification likely will impact the ability of marine calcifiers, such as corals and mollusks, to make their shells and skeletons from the

calcium carbonate dissolved in sea water. Ocean

acidification may indirectly affect fish and marine

mammals through reduced abundance of marine

calcifiers that form the base of the food web and

that provide habitat structure. Ocean acidification

is an emerging concern and an important area for

new research.

Solutions

Addressing the issue of anthropogenic climate

change has two basic components: reducing emissions of the greenhouse gases that are causing global warming, and adapting to the changes that are

already occurring. The first priority, reducing

greenhouse gas emissions, will require reducing the

release of carbon dioxide on a global scale. Among

the approaches are development of alternate energy sources, such as solar, geothermal, wind, and

ocean current, as well as increased development

of nuclear power. Carbon sequestration is a different technical approach, in which the carbon

dioxide produced from burning fossil fuels is sequestered underground instead of released into the

atmosphere.

Energy conservation is an important component of reducing greenhouse gas emissions. This

can be accomplished through many approaches.

Some are technical, such as improving the fuel efficiency of automobiles, power plants, and industrial processes. Others combine technical and societal changes, such as expanding the availability

and use of public transportation. There also are

economic approaches to changing societal patterns

of energy use, such as fuel taxes or selling permits

for carbon dioxide release.

Because anthropogenic climate changes are already occurring, the science and management of

living marine resources must adapt. Some of the

science that will be required is basic research, such

as improving the understanding of how climate

changes are affecting watersheds, estuaries, and

oceans, and the structure and function of the habitats, ecosystems, and species they contain. Improved monitoring that incorporates the latest research findings will enable scientists to better understand the changes that are occurring and their

potential impacts on living marine resources. This

will provide managers with greater lead times and

give them better opportunities to respond to

changing conditions. Applied research for restoring degraded habitats and establishing new ones

also will provide managers with new and better

options for adapting to climate change. Management can also adapt to the higher levels of uncertainty that will accompany climate change. Increasing the levels of protection of vulnerable habitats

and more conservative fisheries management could

help to ensure that stocks remain viable as their

habitats change.

Andy Bruckner, NMFS

Coral reef bleaching off Desecheo Island, Puerto Rico,

in December 2005.

CLIMATE VARIABILITY AND CHANGE
2 4

ISSUE:

INVASIVE SPECIES

AND MARINE DEBRIS

The introduction of non-native species and the

release of marine debris are both unintended consequences of human activities. Because of the lack

of native predators or pathogens, some non-native

species can invade new ecosystems into which they

are introduced and become highly abundant.

NOAA defines marine debris as “any persistent

solid material that is manufactured or processed

and directly or indirectly, intentionally or unintentionally, disposed of or abandoned into the

marine environment or the Great Lakes” (NOAA,

2009). As human activity has increased in aquatic

and coastal environments, rates of introduction

of non-native species and marine debris have increased as well.

Impacts to Habitat and

Living Marine Resources

Invasive species are prevalent in all aquatic

habitat types and regions (EPA, 2008b). For example, about 240 invasive species have become

established in San Francisco Bay alone. Some of

these species are responsible for reducing native

food supplies, eliminating native species, reducing fisheries productivity, and causing substantial

habitat alterations. The invasive sea squirt,

Didemnum, is proliferating on gravel bottoms on

Georges Bank, in highly productive scallop habitats. There is concern that the infestation could

disrupt food chains and interfere with the settlement of scallop larvae (NEFSC, 2006). Non-native species can also carry novel diseases. MSX, a

devastating parasitic oyster disease now widespread

in the Mid-Atlantic, is thought to have arrived in

oysters brought from Japan in the 1950’s. This disease kills oysters, and has been a significant factor

to the drastic decline in oyster harvest in Delaware and Chesapeake Bays. Loss of the oysters also

degrades the reef habitat they provide.

Non-native species are introduced into aquatic

habitats through both intentional and accidental

release. Since the 1800’s, few bodies of water have

been immune to deliberate introductions of species by government agencies and citizens. These

have included various trout and salmon, clams,

oysters, and carp, for recreational, food, or other

purposes. Ballast water, taken onboard at one location to stabilize ships for transit and then released at the destination port, may contain millions of alien eggs, larvae, and microorganisms.

Recreational boaters may also introduce alien species into waterways when they move their pleasure craft between areas without proper precautions. The aquarium trade and accidental releases

from aquaculture operations are additional pathways of non-native introductions.

Marine debris is widely distributed (EPA,

2008c). For example, even in the largely uninhabited Northwestern Hawaiian Islands (NWHI), it

is estimated that about 1,600 metric tons (t) of

debris litter the shorelines. Marine debris results

from numerous sources, including at-sea dumping and land-based littering or illegal dumping. It

can cause significant physical damage to fragile

habitats like coral reefs, introduce toxic substances

and pathogens, and cover salt marshes, wetlands,

and shallow water habitats, making them inaccesAbove: In Hawaii, invasive

algal species have spread to

become the dominant bottom cover in some reef and

coastal areas. The invasive

Cladophora algae in this

photograph has overgrown

and smothered the coral in

this area off Maui.

© Linda Preskitt, Univ. Hawaii

INVASIVE SPECIES AND MARINE DEBRIS
2 5

sible to species that use them and vulnerable to

invasive species.

Marine debris poses a serious threat to the survival of some endangered or threatened sea birds,

marine mammals, and turtles. For example, sea

turtles will ingest plastic bags that closely resemble

jellyfish (their typical food) in appearance and then

eventually die of starvation due to blockage of their

digestive tracts. Discarded or lost fishing gear such

as gillnet panels, traps, crab pots, and longlines

with hundreds of hooks may continue to fish

(“ghost fishing”) for many years.

Solutions

Control of alien species is very difficult once

they have become established in a new habitat, so

preventing new introductions and responding rapidly to newly discovered introductions are very important. The Nonindigenous Aquatic Nuisance

Prevention and Control Act, passed in 1990, aims

to both prevent future introductions and control

existing populations of non-native species. Technological advances, such as onboard use of biocides, filtration, and anti-fouling coatings, as well

as development of shore-based treatment facilities,

are making control of introductions from ballast

water more effective.

More attention is being paid to deliberate introductions. For example, the Asian oyster may

prove less vulnerable to the diseases that have devastated the native oysters in Chesapeake Bay, but

the National Academy of Sciences recommended

a complex research program with strict management controls prior to introduction to rigorously

evaluate the potential benefits and risks of introducing this non-native species (NRC, 2004).

Strict regulations and enforcement efforts exist to restrict at-sea dumping; however, land-based

sources of debris account for about 80% of inorganic waste found in U.S. coastal areas. Local civic

actions such as litter removal and beach clean-ups

have been effective at reducing the amount of debris in the marine environment. Increasing public

awareness can also help. The Ocean Conservancy’s

International Coastal Cleanup program found a

48% decrease in the number of items found per

mile during beach clean-ups between 1994 and

2000 (The Ocean Conservancy, 2002).

NMFS has been actively involved in marine

debris removal from the NWHI since 1996. Over

511 t of derelict fishing gear has been removed as

part of a multiagency partnership supported by

the NOAA Coral Reef Conservation Program and

the Marine Debris Program. A 5-year intensive

effort removed much of the historical debris on

the coral reefs of the NWHI. NOAA was able to

collect 19 t in 2006 in the first year of the maintenance-level effort, but a recent study estimated the

accumulation rate to be 52 t annually. NMFS is

evaluating new technologies, such as remote sensing and unmanned aerial vehicles, to detect and

remove debris at sea before it damages reef ecosystems and impacts protected species.

NOAA

Above: Debris cleaned up

from Midway Atoll, at the far

western end of the Hawaiian

Islands. Discarded fishing

nets make up most of the

debris shown.

Left: Emaciated northern fur

seal entangled with a section of fishing net.

PIFSC, NMFS, NOAA

INVASIVE SPECIES AND MARINE DEBRIS
2 6

ISSUE:

VESSEL TRAFFIC AND NOISE

Vessel traffic can affect marine habitats in a

number of ways. Collisions between vessels and marine mammals or sea turtles, which occur when ships

are transiting these animals’ habitats, can have important impacts on fragile populations of these protected species. Noise is potentially the most pervasive pollutant in marine habitats.

Habitat Impacts

In addition to the introduction of non-native

species from ballast water discussed previously,

vessel traffic has several potential impacts to the

habitats of living marine resources. Near ports,

where deep-draft ocean-going ships frequently

transit through relatively shallow navigational

channels, the re-suspension of sediments by passing ships can reduce water quality by increasing

turbidity and decreasing light penetration, and

toxic chemicals in sediments may be released into

the water column. An additional concern is the

possibility of fuel or oil spills. In 1989, the Exxon

Valdez ran aground in Prince William Sound,

Alaska, and spilled approximately 260,000 barrels of crude oil, contaminating approximately

2,080 km (1,300 mi) of Alaskan shoreline.

Ocean noise is one of the most controversial

and poorly understood habitat threats (U.S. Navy,

2006; Boyd et al., 2008). Noise comes from vessel

traffic, geophysical exploration, active sonars, construction activities, and other sources. It is ubiquitous in the marine environment, and is increasing throughout the oceans by an average of 3

decibels per decade (essentially doubling). Highintensity underwater sound production from research, military, or other activities can reach over

235 decibels, as loud as an underwater earthquake.

Sound of this magnitude can travel great distances

and is detected at high levels even hundreds of

miles from its source.

Impacts to Living Marine Resources

For some species, such as the highly endangered northern right whale, collisions with vessels

are a key factor preventing their recovery. Between

1970 and 1994, vessel encounters were implicated

in 7% of injuries and 28% of known right whale

deaths (Jensen and Silber, 2003).

Above: A ship-struck sei

whale on the bow of a container ship in Chesapeake

Bay.

Cindy Driscoll, Maryland Department of Natural Resources

VESSEL TRAFFIC AND NOISE
2 7

Spills from ships have both acute and chronic

effects. Because oil floats, the most observable impacts of oil spills are to animals that frequent the

surface, such as sea birds and marine mammals.

When it reaches the shore, spilled oil is deposited

primarily in the intertidal and shallow subtidal

zones. Following the Exxon Valdez spill, the largest deposit of oil was in the upper and middle intertidal zones on sheltered rocky shores. Some of

the species affected by that spill included sea otters, harbor seals, and killer whales. Pacific herring, which spawn in shallow coastal habitats, and

salmon, which transit these areas as spawning

adults and out-migrating juveniles, were also significantly affected. Fourteen years after the Exxon

Valdez spill, residual oil was still present in some

habitats. It continues to be a problem for species

that spawn or forage in these areas. This persistence of oil may delay for many years the complete recovery of some habitats or species (Peterson

et al., 2003).

Currently, the impacts of noise on marine

mammals are receiving considerable attention.

Recent mass strandings of beaked whales have

occurred in close association (in time and space)

with military exercises that used high-energy, midfrequency (1–10 kilohertz [kHz]) sonars. Sonar

has also been implicated in altering the singing of

humpback whales, disrupting the feeding of orcas,

and causing porpoises to leap from the water or

panic and flee. There is currently no documented

evidence of ocean noise being the direct physiological agent of any marine mammal deaths, but analysis of fresh, whole animals is rarely possible, and a

definitive diagnosis of the cause of death is often

problematic.

As with marine mammals, many species of fish

use sound to follow migration routes, locate each

other, find food, and care for their young. The

potential impact of noise on fish is relatively unknown. It is clear that animals that use sound for

communication and navigation can easily be affected, but it is less clear what levels will actually

cause damage to animal tissues and hearing organs.

VESSEL TRAFFIC AND NOISE

Solutions

Designating critical habitat areas for marine

mammals vulnerable to vessel collisions, and restricting vessel traffic within those areas, has been

successful at reducing vessel impacts, and will continue to help susceptible populations. Recent regulations limiting the speed of vessels 20 m (65 ft)

or longer to 18.5 km/hr (10 knots) within 37 km

(20 n.mi.) of major Atlantic ports are intended to

protect the northern right whales that occur in

this region (NOAA, 2008). The likelihood of spills

and other impacts to habitat from passing ships

can be minimized through improved navigation

and port facilities.

Because the potential impacts of noise have

become a concern only recently, research is needed

to better define these impacts and to develop approaches to minimize the impacts that are documented.

The U.S. Navy’s Atlantic Undersea Test and Evaluation

Center (AUTEC) range in the

Bahamas, where a NOAAled international team,

funded primarily by the U.S.

Navy, is studying the behavioral responses and relative

sensitivities of several marine mammals to sonar

(Boyd, et al., 2008). This

high-altitude image shows

Andros Island (center) surrounded by shallow (turquoise) water to the left side

and very deep water to the

right (a trench called Tongue

of the Ocean). The AUTEC

range is in the middle of the

trench, and has 82 hydrophones deployed over 1,554

km2 (600 mi2) of the sea

floor.

NASA
2 8

CONCLUSIONS

Managing habitat through conservation and

protection is critical because of the living marine

resources that habitat supports. An effective program requires components that protect and conserve remaining habitat, restore damaged or lost

habitat, and build or enhance habitat where there

are opportunities to do so. These actions require

the engagement and support of an informed citizenry and government agencies with habitatconservation mandates and the resources needed

to carry them out.

Scientific information and the scientists that

generate it are key to effectively managing habitat. Understanding the relationships between species and habitats, knowing where and how much

habitat exists, and rigorously monitoring and assessing its condition can provide the scientific basis for managing habitat. However, this information can only be effective in informing public

policy when it is communicated to resource managers, stakeholders, and the public in a timely

manner and in forms that are appropriate to the

specific audiences.

To prevent further impacts from habitat degradation, fragmentation, and loss, the habitats that

remain can be conserved and/or protected through

legislation and vigorous enforcement. Although

more than 1,000 areas within U.S. waters are

granted some level of special protection by Federal or state governments, only about 1% of the

ocean within U.S. jurisdiction qualifies as a marine protected area, and only about 10% of that

carries the highest level of protection, where fishing and other extractive activities are precluded.

Clearly there is the potential to protect more area,

and to provide high-priority areas with a greater

level of protection. However, conserving and protecting habitat does not have to be accomplished

only by setting aside large areas of habitat. Other

management options also exist, such as fishery

time/area closures, avoiding certain activities in

sensitive areas (e.g. banning bottom trawling over

deep-coral beds, but allowing fishing using other

gears that do not contact the bottom), and developing alternative methods or new technologies that

reduce or eliminate the most deleterious impacts.

Creating or restoring habitat is usually much

more expensive and less effective than conserving

© Jiangang Luo, University of Miami

Left: Steller sea lions hauled

out on Benjamin Island,

near Juneau, Alaska.

Right: Mangrove roots provide essential habitat for

many species, such as in this

mangrove habitat at Elliott

Key in Biscayne Bay, Florida.

NMFS
2 9

habitat that already exists and is functioning. The

science of creating and restoring habitats is relatively new, so more research is needed to develop

and evaluate restoration methods. When habitat

is created or restored, it should be done with a

valid scientific purpose and experimental design,

so that effectiveness can be evaluated through

monitoring and additional corrective actions undertaken if they prove necessary. To ensure restoration success, NOAA’s Restoration Center employs technical staff to improve project design,

advance restoration techniques, and use ongoing

scientific monitoring to evaluate restoration

projects and assure efficient use of restoration

funds.

This Policymakers’ Summary, and the complete

Our Living Oceans: Habitat report from which it

is derived, provide a comprehensive overview of the

habitat issues that are affecting the living marine resources of the United States, and the state of the scientific information on these issues. The intent is to

provide scientifically valid information in a form

that can be used not only by scientists, but also by

stakeholders, policymakers, students, and the general public.

The overall message in these reports is mixed.

The United States still possesses a considerable

amount of functioning habitat, which supports

substantial harvests of fishery resources and populations of protected species. However, there has

been substantial loss and degradation of habitat

in many areas, especially where human activities

occur. The cumulative impacts of these losses cannot readily be quantified, but they are undoubtedly considerable, especially on urbanized watersheds, estuaries, and coasts.

In order that our Nation can continue to benefit from abundant living marine resources, our

society needs to place a high priority on managing habitat. Human populations and economic activities will continue to expand, placing ever-increasing demands on the environment and the

habitats it contains. Gaps in the relevant scientific

information must be filled, and the information

communicated, such that our decisionmakers can

be appropriately informed as policy is developed

and implemented. The National Marine Fisheries

Service has developed the Our Living Oceans series of reports to contribute to these vital processes.

Biogeography Team, CCMA, NOS, NOAA

Left: Coral reef and fish in

the Pacific Islands.

Right: Southeast Alaska wetland and estuarine habitat

supports many fish species

at critial times in their life

cycles.

Mandy Lindeberg, NMFS
3 0

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