Land-Use Changes and the 

Physical Habitat of Streams— 

A Review with Emphasis on Studies within 

the U.S. Geological Survey FederalState Cooperative Program

Land-Use Changes and the 

Physical Habitat of Streams— 

A Review with Emphasis on Studies within 

the U.S. Geological Survey FederalState Cooperative Program

U.S. Department of the Interior

U.S. Geological Survey

Circular 1175
Stream habitats in the United States 

are highly variable and have a wide 

range of potential land-use stressors.

Cover photograph left: The Cascade Mountains of 

Oregon have high-gradient, coarse-bedded streams.

Cover photograph right: The Chickahominy River in the 

Coastal Plain of Virginia is a low-gradient, sand-bed 

stream. 
Land-Use Changes and the Physical Habitat of Streams—

A Review with Emphasis on Studies within the 

U.S. Geological Survey Federal-State Cooperative Program

By Robert B. Jacobson, Suzanne R. Femmer, and Rose A. McKenney

Circular 1175
Library of Congress Cataloging in Publication Data

Any use of trade, product, or firm names in this report is for identification purposes 

only and does not constitute endorsement by the U.S. Government.

For sale by U.S. Geological Survey, Information Services,

Box 25286, Federal Center,

Denver, CO 80225

Reston, Virginia 2001

U.S. DEPARTMENT OF THE INTERIOR

GALE A. NORTON, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

Jacobson, Robert B.

Land-use changes and the physical habitat of streams : a review with emphasis on studies within the U.S. Geological Survey Federal-State cooperative program / by Robert B. Jacobson, Suzanne R. Femmer, and Rose A. McKenney.

 p. cm. — (Circular ; 1175)

Includes bibliographical references (p. ).

ISBN 0-607-94327-0

1. Stream ecology. 2. Land use — Environmental aspects. 3. Habitat (Ecology) —Modification.

I. Femmer, Suzanne R. II. McKenney, Rose A., 1962- III. Title. IV. U.S. Geological Survey circular ; 1175.

QH541.5.S7 J23 2000

577.6’4 — dc21 00-061784
Contents III

CONTENTS

Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

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

The Federal-State Cooperative Program and Physical Stream Habitat Investigations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Factors Affecting Physical Stream Habitat. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Definition and Classification of Physical Stream Habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Abiotic and Biotic Factors Affecting Habitat Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Formation and Stability of Physical Stream Habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Channel Morphology and Stream Habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Channel Equilibrium and Stream Habitat. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Channel Disturbance and Adjustment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Habitat Disturbance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Land-Use Induced Disturbance of Physical Stream Habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Upland Land-Use Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Riparian Land-Use Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Investigating the Links Between Land Use and Physical Stream-Habitat Changes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Historical Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Associative Approaches to Land Use—Habitat Links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Associations for Assessing Habitat Availability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Associations for Water-Quality and Environmental Assessments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Process Studies of Land Use—Habitat Links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Modeling Links between Land Use and Physical Stream Habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Basin-Scale Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Channel-Scale Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Land-Use Changes and the Physical Habitat of Streams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Selected References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Special Sections: Multidisciplinary USGS Cooperative Studies of the Links 

Between Land Use and Physical Stream-Habitat Changes

Hydrologic Disturbance in an Agricultural-Urban Basin—Big Darby Creek, Ohio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12–13

Geomorphic Instability and Sediment Loads—Wisconsin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16–17

Water Withdrawals and Maintenance of Floodplain Ecosystems—Florida . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20–21

Habitat in Channelized Streams—Tennessee . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24–25

Riparian Vegetation and Maintenance of Physical Habitats—Missouri. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26–27

Establishing Land-Use History and Habitat Links—Missouri. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32–33

Land-Use Characteristics and Aquatic Community Structure—Ozark Plateaus NAWQA Study Unit . . . . . . . . . . . . . . . . . . . . . . . . . . 38–39

Mill Creek Cattle Exclosure Study—Pennsylvania . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42–43

Measuring the Effect of Boat Wakes on Bank Erosion and Salmon Habitat—Alaska . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44–45

Climate Change Effects on Sediment and Streamflow—Colorado . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48–49

Minimum Instream Flow Modeling—Virginia and Washington . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50–51
IV Contents

Illustrations

1. Photograph showing deposition of fine sediment and channel instability downstream of an instream 

aggregate mine, North River, Missouri . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

2. Map showing the locations of multidisciplinary USGS cooperative studies, which are discussed in this report, that are

investigating the links between land use and physical stream-habitat changes, . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

3. Diagrams showing scales of processes that link land use to stream habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

4. Map showing channel changes in Little Piney Creek . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

5. Graphs showing types of equilibria, disturbance, and response patterns for streams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

6. Diagram showing effect of oversteepening streambanks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

 7–8. Photographs showing:

7. Hydrologic changes due to urbanization in a drainage basin can have severe effects on stream habitat . . . . . . . . . . . . . . . . . . . 14

8. Upland land-use processes in rural areas can decrease infiltration, increase runoff,

and increase soil erosion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

9. Graph showing percentage of rainfall in runoff estimated from the Soil Conservation Service (1972) 

curve number method for typical rural land uses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

10. Photograph showing landslides on intensely grazed slopes in the Appalachian Mountains of West Virginia. . . . . . . . . . . . . . . . . . 18

11. Graph showing predicted ratio of soil erosion from specified land-use classes to soil erosion expected from 

natural woodland . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

12–14. Photographs showing:

12. Dams and reservoirs directly affect stream habitat by controlling quantity and timing of water discharge and by

decreasing sediment yield to downstream channel segments—Gavins Point Dam, Missouri River near Yankton, 

South Dakota . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

13. Aggregate mining in stream channels or in riparian zones can affect stream habitats directly . . . . . . . . . . . . . . . . . . . . . . . . . . 22

14. Channelization has resulted in a deeply incised stream channel on Cane Creek, western Tennessee. . . . . . . . . . . . . . . . . . . . . 23

15. Graphs showing bathymetry and velocity data from a navigational reach of the Missouri River near 

Rocheport, Missouri. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28–29

16. Photograph showing accumulations of large woody debris on Little Piney Creek, Missouri . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

17. Map showing channel positions of the Missouri River near Glasgow, Missouri, 1879 and 1991 . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

18. Photograph showing how detailed measurements are made to study land-use effects on stream geomorphology

and habitat in the Ozark region of Arkansas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

19. Diagrams showing experimental flood on the Grand Canyon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

20. Maps and graphs showing example of using a two-dimensional hydraulic model to determine areal distributions 

of velocity and depth pairs for an entire reach, same bankfull discharge, for two different channel configurations . . . . . . . . . . . . 52

Tables

1. Matrix of typical channel and habitat responses to changes in land use in upland and riparian areas. . . . . . . . . . . . . . . . . . . . . . . . 55–57
Contents V

CONVERSION FACTORS AND ABBREVIATIONS

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch

meter (m) 3.281 foot 

kilometer (km) 0.6214 mile 

Area

square meter (m2) 0.0002471 acre

square kilometer (km2) 247.1 acre

square kilometer (km2) 0.3861 square mile

Volume

cubic meter (m3) 264.2 gallon 

Flow rate

cubic meter per second (m3/s) 35.31 cubic foot per second 

Temperature in degrees Fahrenheit ( ̊F) may be converted to degrees Celsius ( ̊C) as follows:

 ̊C=( ̊F-32)/1.8

Sea level: In this report "sea level" refers to the National Geodetic Vertical Datum of 1929 (NGVD of 1929)—a geodetic datum derived from a general

adjustment of the first-order level nets of both the United States and Canada, formerly called Sea Level Datum of 1929.

Altitude, as used in this report, refers to distance above or below sea level.

Transmissivity: The standard unit for transmissivity is cubic foot per day per square foot times foot of aquifer thickness [(ft3

d)/ft2]ft. In this report, the

mathematically reduced form, foot squared per day (ft2

/d), is used for convenience.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 25  ̊C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or micrograms per liter (μg/L).

NOTE TO USGS USERS: Use of hectare (ha) as an alternative name for square hectometer (hm2

) is restricted to the measurement of small land or

water areas. Use of liter (L) as a special name for cubic decimeter (dm3

) is restricted to the measurement of liquids and gases. No prefix other than milli

should be used with liter. Metric ton (t) as a name for megagram (Mg) should be restricted to commercial usage, and no prefixes should be used with it.

 1

 Figure 1. Direct disturbances of the stream

channel can result in the deposition of fine

sediment and channel instability as shown here

downstream of an aggregate mine on the North

River, Missouri. Some changes in stream habitat

are distinct and clearly associated with a

particular land-use disturbance.

Land-Use Changes and the Physical Habitat of Streams—

A Review with Emphasis on Studies within the U.S. Geological Survey 

Federal-State Cooperative Program

By

Robert B. Jacobson, Suzanne R. Femmer, and Rose A. McKenney 

ABSTRACT

Understanding the links between land-use changes and 

physical stream habitat responses is of increasing 

importance to guide resource management and stream 

restoration strategies. Transmission of runoff and sediment to streams can involve complex responses of 

drainage basins, including time lags, thresholds, and 

cumulative effects. Land-use induced runoff and sediment yield often combine with channel-scale disturbances that decrease flow resistance and erosion 

resistance, or increase stream energy. The net effects of 

these interactions on physical stream habitat—depth, 

velocity, substrate, cover, and temperature—are a challenge to predict. Improved diagnosis and predictive 

understanding of future change usually require multifaceted, multi-scale, and multidisciplinary studies 

based on a firm understanding of the history and processes operating in a drainage basin. The U.S. Geological Survey Federal-State Cooperative Program has been 

instrumental in fostering studies of the links between 

land use and stream habitat nationwide.

INTRODUCTION

Land-use changes have occurred to some extent almost 

everywhere in North America since European settlement. Changes in vegetative cover, disturbance of soils, 

and the loss of wetlands have created the substantial 

potential for altered runoff and sediment yield in many 

regions. Disturbances of streams by activities such as 

channelization, aggregate mining, livestock grazing, 

and dams have directly affected channel morphology 

and streamflow characteristics. Changes in runoff and 

sediment yield to streams and direct disturbances of 

channels can severely alter physical stream habi-
2 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

tat—the template of temperature, turbidity, water depth, 

current velocity, channel substrate, and cover that supports the stream ecosystem (fig. 1). Cover, such as boulders, root wads, or submerged vegetation, provides 

concealment and protection to organisms in an aquatic 

system.

Habitat can be conceptualized as the physical and 

chemical characteristics of a stream that determine suitability for habitation and reproduction of stream organisms. The characteristics, volume, spatial arrangement, 

and variation of habitat over time can be fundamental 

controls that determine which organisms can survive or 

thrive in a stream and, therefore, may function also as 

preliminary controls on biotic interactions such as competition or predation.

Physical habitat change has been recognized as a key 

factor in degradation of many stream ecosystems (Jeffries and Mills, 1990; Waters, 1995). At the same time, 

the land-use changes that have caused physical-habitat 

degradation—such as agriculture, mining, forestry, and 

urbanization—have substantial economic benefits. To 

evaluate the balance between economic and ecosystem 

values, there is a need to understand the process links 

between land-use change and physical habitat change. 

Improved understanding of these links may lead to 

more effective resource management and stream restoration strategies.

The links from land-use change to alteration of physical 

habitat and subsequently to changes in the stream biota 

can be complex and difficult to trace. Processes and 

rates of the processes that form the links from land use 

to habitat vary with time and space. Links can be indirect and cumulative, such as the downstream accumulation of sediment produced by widespread, lowmagnitude soil erosion over a drainage basin. In contrast, links can be clear and direct, such as the effect of 

a dam on discharge flow duration. In many situations, 

key links between land-use changes and physical-habitat changes have to be identified from a confusing mixture of multiple land-use changes and natural 

disturbances.

While some habitat-biota links or portions of links have 

been well established, others are poorly understood. 

Many aquatic ecologists view availability of particular 

habitats as a necessary but insufficient condition for 

biotic responses. Physical and chemical habitat determine potential for biotic communities, but realization 

of the potential is highly dependent on how and when 

species use habitat, on extrinsic disturbances like floods 

or droughts, and on biotic interactions that determine 

population dynamics.

States for two broadly defined applications. The first 

application is for management of biological resources, 

principally for sport and commercial fisheries, and 

more recently for threatened and endangered species. 

Recognition of the habitat requirements of such species 

and the processes that generate and maintain those habitats gives managers the knowledge to mitigate adverse 

effects and promote production. The second broad 

application is in bioassessment of water quality. Bioassessment recognizes the utility of stream biota to provide an overall index of stream health and to integrate 

the effects of multiple stressors. Because biota give an 

integrated response to chemical and physical changes in 

their environment, physical habitat must also be evaluated to interpret causes for biotic responses. Thus, bioassessment of water quality requires that the effects of 

physical habitat variations are accounted for. The need 

for understanding physical habitat was summarized by 

Rankin (1995) in a discussion of habitat monitoring:

“Analyses performed in Ohio suggest that without biosurvey and habitat data there is a high risk of missing 

non-chemical and chemical impacts to streams.... There 

is a smaller but still significant risk of ‘finding’ a water 

quality impact where one really does not exist when 

[habitat] monitoring data are insufficient. This could 

result in a regulatory action that might cost hundreds of 

thousands of dollars or more to an entity, with costs 

passed along to consumers.”
THE FEDERAL-STATE COOPERATIVE PROGRAM AND PHYSICAL STREAM HABITAT INVESTIGATIONS 3

THE FEDERAL-STATE COOPERATIVE PROGRAM AND 

PHYSICAL STREAM HABITAT INVESTIGATIONS

Understanding the links between land-use changes, 

physical habitat changes, and biotic responses requires 

a multidisciplinary scientific approach combining 

hydrology, sediment transport, geomorphology, and 

ecology. Because the links are sensitive to specific landscape characteristics, disturbance processes, and disturbance histories, improved understanding generally 

requires a field-oriented approach that is tailored to specific situations. Within the constraints indicated by the 

field-oriented approach, theoretical and computational 

models can be used to enhance understanding of the 

links.

Through the Federal-State Cooperative Program, the 

U.S. Geological Survey (USGS) has participated in 

many studies that are intended to develop improved 

understanding of the processes linking land-use and 

physical stream-habitat changes. These studies include: 

• Historical studies to diagnose how habitats have 

changed in response to past land-use changes;

• Associative studies of correlations among drainage-basin scale land-use characteristics, 

• Process studies of links between land use and habitat, and

• Modeling studies of the links between land use and 

habitat.

By developing scientific studies in partnership with 

State and local agencies, the USGS has been able to 

apply multidisciplinary expertise and a field-oriented 

scientific approach throughout the United States to help 

integrate concerns of stream ecosystem management 

with concerns of land-, mineral-, and water-resources 

management.

The purpose of this report is to provide a general framework for understanding links between land-use and 

physical stream-habitat changes. Complete discussion 

of the wide range of topics that form the framework 

introduced here is beyond the scope of this report. References are provided to guide the interested reader to 

more complete treatments in the hydrology, ecology, 

and geomorphology literature. This framework is supplemented with a discussion of multidisciplinary 

approaches to investigating links, with illustrative 

examples from USGS cooperative studies (figure 2).

FACTORS AFFECTING PHYSICAL STREAM HABITAT

Physical stream habitat is studied and defined at multiple scales. The instream microhabitat is within the reach 

scale, which is a subcategory of the segment scale that 

exists within the basin scale. The drainage basin scale 

exists within gross classification units such as physioPages 16–17

Pages 12–13

Pages 48–49

Pages 42–43

Pages 50–51

Pages 44–45

Pages 24–25

Pages 26–27 

and pages 32-33

Pages 20–21

Pages 38–39

Pages 48–49

Figure 2. Locations of multidisciplinary USGS cooperative studies, which are discussed in

this report, that are investigating the links between land use and physical stream-habitat

changes.
4 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

graphic settings and ecosystems, although most landuse studies are measured and managed at the drainage 

basin scale or finer.

This hierarchy forms the basis for river- and streamhabitat classifications. The hierarchy also implies a set 

of process links: instream habitats are formed by fluxes 

of water, sediment, and energy; the spatial, temporal, 

and material characteristics of these fluxes are determined by factors at higher levels of the hierarchy. Sufficient understanding of these process links could allow 

the prediction of habitat conditions from knowledge of 

the hierarchical controls on a particular stream reach.

The process links that form habitat are insufficiently 

known. This results from the inherent complexity of 

geomorphic systems in which spatial variations in geologic characteristics, physiography, and vegetative covers are combined with temporal variations of climate 

and tectonics, which are compounded by the “complex 

response” of drainage basins due to lags, thresholds, 

and cumulative effects. These factors present real challenges to our understanding of the links between landscape changes and physical stream-habitat changes.

In addition, the link from physical habitat to habitat use 

by stream organisms presents complications and challenges to our understanding. Stream ecologists recognize that habitat is a necessary foundation for many 

stream communities, but disturbance regime and biotic 

interactions also affect community structure and habitat 

use. This section of the report presents definitions and 

classifications of rivers and stream habitat, discusses 

the physical links of habitat formation and disturbance 

within geomorphic systems, and reviews concepts of 

the role of physical habitat in structuring stream communities.

Definition and Classification of 

Physical Stream Habitat

Physical habitat is a general term for the surroundings 

where organisms live. In streams, physical habitat 

includes water temperature, turbidity, water depth, current velocity, channel substrate, and cover. Characteristics considered to be part of physical habitat overlap 

somewhat with water-column chemical characteristics 

such as pH, dissolved oxygen, nutrients, and other dissolved constituents. For the purposes of this report, 

however, physical habitat is limited to those characteristics that do not necessarily involve chemical proccesses.

Physical habitats are classified to inventory the range of 

physical characteristics between and within stream systems. Classification systems subdivide the continuum 

of a stream into units with similar characteristics, using 

consistent criteria to define and separate habitat types. 

In this manner, habitat availability and quality can be 

evaluated systematically. Systematic classification aids 

in statistical sampling design for population estimates, 

in improving understanding of ecological functioning, 

and in developing restoration strategies (Hawkins and 

others, 1993).

Because classification systems are used for planning 

and management over a range of spatial scales, habitat 

classification systems exist for a range of spatial scales. 

The classification scale used depends on the level of 

information needed. At the broadest levels of classification, ecoregions and physiographic provinces define 

geologic and climatic constraints on river systems (for 

example, Pflieger, 1989). Classification of streams at 

the drainage-basin scale includes classification of areal 

features of the drainage basin and linear features of the 

stream network. The areal features of basins typically 

are classified according to geology, geomorphology, 

soils, climate, vegetation, and land use. The stream system within a basin can be classified based on the longitudinal profile and channel network characteristics such 

as stream order.

Within stream systems, a finer scale of classification 

usually is achieved by subdividing the channel into segments that have uniform bedrock and that exist between 

tributary junctions or point sources of disturbance (Frissell and others, 1986). Uniformity of bedrock and 

hydrologic characteristics defines a range of channel 

characteristics for a particular segment. Within segments, reaches are defined as lengths of stream that lie 

between substantial changes in channel morphology, 

valley width, and riparian vegetation. In streams with 

mobile beds and banks, reaches generally have multiple 

occurrences of repeating riffle-pool or step-pool 

sequences. Hence, reaches usually are defined as 

lengths of stream that contain representations of all habitat types that exist within a segment. The reach scale 

commonly is used to investigate stream communities as 
FACTORS AFFECTING PHYSICAL STREAM HABITAT 5

Figure 3. Scales of processes that link land use to stream 

habitat. Land use at the scale of drainage basins determines 

runoff and sediment transmitted through the drainage network. 

Segments are parts of the drainage network between 

substantial tributaries and are characterized by two or more 

repeating macrohabitats and relatively uniform channel 

pattern. Macrohabitats are repeating parts of the stream 

channel within which depth, velocity, and substrate are 

uniform. Macrohabitats are bounded by sharp gradients of 

depth., velocity, and substrate in transition to adjacent 

macrohabitats. Effects of land-use change on habitat are 

typically measured at the reach scale in terms of changes to 

macrohabitats.

well as to describe channel morphology (Frissell and 

others, 1986). The Rosgen classification system (Rosgen, 1996) emphasizes channel planform and cross-sectional channel morphology to classify discrete stream 

types. This system has been widely used to classify 

streams at the reach and segment scales.

At the next finer scale, reaches can be subdivided into 

habitat units or macrohabitats. Macrohabitat classifications recognize the existence in streams of 

“semi-discrete areas of relatively homogeneous 

depth and flow that are bounded by sharp physical gradients...” (Hawkins and others, 1993, p. 

4). These areas are the familiar riffles and pools 

and subdivisions based on morphology, depth, 

velocity, turbulence, substrate, and cover (fig. 

3). Many macrohabitat classification schemes 

exist, perhaps because the vast range of channel 

characteristics and applications precludes any 

one particular classification scheme. Some 

effort is being applied to develop overarching, 

hierarchical classification systems that will 

resolve useful definitions at a range of scales 

(for example, Hawkins and others, 1993; 

Rabeni and Jacobson, 1993a).

Although stream and habitat classifications are 

useful for many inventory applications, classification is limited in what it can contribute to 

understanding of stream habitats because it is a 

static portrayal of a dynamic system (fig. 4). 

Habitat changes result inevitably from channel 

dynamics, and most stream channels exhibit 

changes over time intervals of minutes to 

decades. The understanding and management 

of physical habitat requires substantially more 

than a static classification of streams and associated habitats. The Rosgen system of classification, for example, has been subject to 

criticism specifically because it does not adequately consider channel dynamics and 

responses to disturbance (Miller and Ritter, 

1996). At the reach scale, the distribution of 

macrohabitats varies through time with individual flood events and as the channel migrates 

and adjusts to sequences of channel-forming 

flows, land-use changes, and random hydrologic occurrences. A process level understanding of factors that control macrohabitat 

formation, evolution, and stability would be 

useful extensions to habitat classification systems.

Drainage-basin scale—Hundreds

 to thousands of kilometers

Made up of segments

Segment scale—Tens to

 hundreds of kilometers

Made up of reaches

Reach scale—Tenths to

 tens of kilometers

Made up of macrohabitats—

 Riffles, pools, backwaters,

 and glides

Riffle

Riffle

Riffle

Pool

Pool Glide

Glide

Backwater

Forewater

Backwater
6 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

Abiotic and Biotic Factors Affecting 

Habitat Use

Numerous studies have documented that stream community structure relates directly to the quantity and 

quality of physical habitat in channels. For example, 

Gordon and others (1992) state: 

“Patterns of physical habitats are created along a 

stream and within the pools, riffles and boulder clusters 

within particular stream reaches. It is to these patterns 

that stream biota respond and adapt. An individual species will have a range of tolerance to any given factor, 

with some factors more critical for some species than 

others. Thus, if the physical factors are known, predictions can be made about the abundance and/or diversity 

of organisms.”

Ecologists have documented that many stream organisms are highly dependent on stable, spatially heterogeneous habitats, and studies on individual species have 

demonstrated that many have strong preferences for 

particular combinations of flow depth, velocity, and bed 

material. In general, diversity of species in stream communities increases with an increase in the diversity of 

physical habitat available for use (Gorman and Karr, 

1978; Schlosser, 1987; Jeffries and Mills, 1990).

Many organisms show specific preferences for particular physical habitats at different life stages. For example, young fish use macrophyte beds and edgewater 

habitats for nursery areas, juveniles use channel margins for foraging and avoiding predation, and the adult 

life-stage use pool, edgewater, and large woody debris 

habitat (Lobb and Orth, 1991). Hence, physical habitat 

controls may limit only particular life stages of an 

organism.

Abiotic conditions are not static, however. Habitat is 

subject to physical disturbance events of varying magnitudes that may force biota to inhabit nonpreferred 

areas of their environment or alter food sources or biotic 

interactions. Extreme events (floods or droughts) can 

eliminate the biota or the habitat, or both, thereby 

requiring longer periods of recovery (Power and others, 

1988). These stochastic events can enable previously 

nondominant species to take advantage of and establish 

dominance in the community. Community organization 

also experiences cyclic or episodic fluctuations due to 

temperature, sunlight exposure, and food supply under 

natural conditions.

In addition to the magnitude, frequency, and persistence 

of disturbances, the periodicity or lack of periodicity of 

disturbances can be critical factors in determining community structure and consequent habitat use. Some 

1938

1948

1955

1964

1976

1989

0

0 0.5 1 MILE

0.5 1 KILOMETER

Valley wall 

Flow

North

EXPLANATION

37o52' 37o51'

91o51'30"

91o52'

Figure 4. Channel changes in the Little Piney Creek, Missouri, a dynamic stream system, 

are apparent in this illustration of 50 years of record. Distinct longitudinal differences in 

inherent channel stability within the river segment are apparent. Stream classification 

systems for application to habitat evaluations should include measures of stability 

(Jacobson and Pugh, 1997). The location of Little Piney Creek is shown in the section 

“Establishing Land-Use History and Habitat Links—Missouri” on p. 32.
FACTORS AFFECTING PHYSICAL STREAM HABITAT 7

communities are structured by frequent flow disturbances that create new and possibly greater numbers of 

niches available for use, or suppress a normally dominant species (Resh and others, 1988). Disturbances that 

occur immediately after spawning can lead to longer 

population recovery times than those that occur during 

or prior to spawning (Detenbeck and others, 1992). On 

the other hand, removal of flood disturbances by stream 

regulation can decrease fish species diversity in some 

streams (Gehrke and others, 1995). The effects of disturbance and varying community responses complicate 

the ability to predict community structure based on 

physical habitat alone.

The effects of physical habitat and disturbance are 

interrelated with biotic interactions in the determination 

of the stream community. Behaviors such as colonization processes, species migration, competition (for food 

and space), and predation can be major determinants in 

structuring stream communities. Intraspecie and interspecie competition affects the location and density of 

organisms in streams as they compete for the same 

space or food source. This competition may determine 

how many species can occupy the same physical space. 

Predation affects the community structure in ways similar to competition. Predation can have effects on the 

individual survival and on community diversity (Jeffries and Mills, 1990). From observation and experimentation, Power and others (1985) determined that 

grazing, predation, and predator avoidance in conjunction with seasonal and successional events exerted rapid 

and strong effects on the distribution patterns of the fish 

and algae in a prairie-margin stream. Power and others 

(1988) concluded that the distribution of stream organisms in relation to physical habitats is strongly affected 

by interactions with other organisms.

While species diversity often correlates well with physical habitat diversity, the relation between species abundance (populations) and physical habitat is less clear. 

Often a linear relation between quantity of habitat available and species abundance is assumed. In fact, evidence in some stream ecosystems is that habitat is a 

limiting factor in abundance only to a particular population or density. After that point, biotic factors become 

limiting. For example, Probst and others (1984) concluded that additional habitat elements in a warmwater 

stream in Missouri could result in increased densities of 

centrarchid fishes to the point where competition for 

food would limit population densities.

Reconciliation of abiotic and biotic perspectives on 

stream community ecology is difficult because exceptions to any generalization will exist. However, the 

importance of physical habitat in structuring communities is well established. Many stream ecologists consider physical habitat to be the major determinant of 

stream community potential (Schlosser, 1987; Plafkin 

and others, 1989). The template of physical habitat is a 

necessary first-order condition that determines the 

expression of second-order biotic effects such as competition and predation.

Formation and Stability of Physical 

Stream Habitat

Channel morphology and sediment characteristics—the 

building blocks of physical habitat—result from adjustments of the channel to the water discharge and sediment load imposed on the channel from upstream and 

from changes in bank strength and flow resistance. Literature is abundant, in fluvial geomorphology, on the 

factors that determine channel characteristics, on concepts of equilibrium channel forms, and on how channels adjust when these factors are altered. However, 

stream ecologists recognize that the conventional geomorphic view of a river does not resolve characteristics 

of importance to fish and invertebrates (Bisson and others, 1982; Hawkins and others, 1993). That is, there are 

spatial features smaller than riffles and pools and temporal fluctuations more frequent than annual floods that 

determine the structure and function of stream ecosystems. Disturbance and adjustment of channel morphology almost always involve changes in habitat quantity, 

quality, or stability and, thereby, affect stream biotic 

communities. The concepts of equilibrium channel 

form, disturbance, and adjustment underlie understanding of how land-use changes are linked to physical 

stream habitat.

Channel Morphology and Stream Habitat

Channel morphology results from interdependent 

adjustment of channel characteristics to the discharge 

of water and sediment load supplied to the channel, 

tempered by effects of bank strength and hydraulic flow 

resistance. In some channels, morphology is deter-
8 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

mined almost completely by external effects such as 

landslides, bedrock walls, or engineering structures. As 

external constraints are removed from a channel, 

adjustment of depth, width, and slope takes place to the 

extent that the river can erode its bed and banks or 

deposit sediment supplied to it from upstream. Channels formed in erodible, relatively homogeneous sediments (for example, alluvial channels) are considered 

self-formed and attain familiar characteristic forms, 

such as braided, meandering, or straight. Empirical 

studies of river systems have defined broadly the gradient, discharge, and sediment load that determine channel patterns and the associated physical stream habitats 

(Leopold and Wolman, 1957).

Channel adjustments in cross-sectional-morphology, 

planform, and longitudinal profiles are thought to occur 

by depth, width, and slope adjustments constrained to 

minimize work and variation in the distribution of work 

(Leopold, 1994). The adjustments result in remarkably 

consistent relations between channel cross-sectional 

measures such as bankfull depth, bankfull width, and 

discharge. These statistical models of hydraulic geometry form another broad level of understanding of how 

physical stream habitats are formed.

Many of the features and characteristics of channels 

that relate to habitat, however, are finer than the rifflepool scale and comprise the outliers of statistical 

hydraulic geometry models. These features are formed 

by nonideal processes such as hydraulic interactions 

with vegetation, large woody debris, bedrock outcrops, 

cohesive bank sediments, debris introduced by slope 

processes, and bars and bedforms relict from extreme 

floods. Understanding the formation and stability of 

macrohabitat features requires more detailed understanding of vegetation dynamics, hydraulics of flow 

around vegetation and obstructions, processes of bank 

erosion of heterogeneous materials, and the effects of 

magnitude, frequency, and sequence of sediment-transporting events. Computational hydraulic and sedimenttransport models promise to provide insight into the 

processes of how channel morphology adjusts to discharge and sediment load in idealized channels (Smith 

and McLean, 1984; Wiele and others, 1996). Research 

into understanding hydraulics at the macrohabitat scale 

is a fairly new and growing discipline of fluvial geomorphology.

Channel Equilibrium and Stream Habitat

The concept of equilibrium in a stream system is valuable because it is a shorthand description of the state of 

the system and expected change in morphology. The 

concept of dynamic equilibrium (Hack, 1960) acknowledges the fact that no stream system is static, but exhibits fluctuations of morphological characteristics in 

response to climatic, land-use, and random disturbances. A stream in dynamic equilibrium is expected to 

show fluctuations about a mean condition. Conversely, 

a stream described as disturbed is expected to show 

directional change in some of its characteristics as it 

readjusts.

The concept of equilibrium helps in evaluation of when 

and where ongoing adjustments of the fluvial system 

should be a concern to stream biota. Every stream, over 

time, tends toward a state in which it accommodates 

discharge and sediment load by adjusting its interdependent hydraulic variables (gradient, width, depth, 

velocity, and hydraulic roughness). This tendency 

toward adjustment has been called quasiequilibrium

(Leopold and Maddock, 1953). The remarkably consistent patterns of variation of stream channel morphology 

with discharge is evidence that such adjustments occur 

as a result of fundamental physical processes (Leopold, 

1994). However, the adjustment is not instantaneous, 

and, therefore, channels can exist in nonequilibrium 

states for substantial periods of time.

The physical characteristics of a stream (for example, 

discharge, depth, velocity, and channel cross-sectional 

shape) affect stream organisms by defining habitat volume, habitat quality, and disturbance magnitude and 

frequency. Hence, the question of whether a stream is in 

physical equilibrium is essential to understanding the 

quantity, quality, and stability of habitat available to 

stream communities. An evaluation of the physical 

equilibrium of a stream can indicate whether trends in 

biotic communities result from physical adjustments of 

the river, rather than from independent biological or 

chemical processes.

Practical consideration of equilibrium in fluvial systems requires that some limits are set on time scale, spatial scale, and magnitude of events that are considered 

to depart significantly from equilibrium values. As discussed by Schumm and Lichty (1965), detection of 
FACTORS AFFECTING PHYSICAL STREAM HABITAT 9

trends and magnitude of variation depend on the spatial 

and temporal frames of interest. In a decadal time 

frame, a 100-year flood is likely to cause significant 

variation in channel characteristics; however, if the time 

frame of interest is millennial, this same flood probably 

would create insignificant background variation. If the 

spatial frame of interest is a particular pool-riffle pair, 

aggradation of that pool would be considered a significant event; however, if the spatial frame is that of a 

stream segment of several tens of kilometers, the fate of 

one pool may be insignificant, or aggradation of one 

pool may be offset by scour of another for zero net 

effect.

The spatial and temporal frames of interest in stream 

habitat evaluation can be narrowed by considering spatial and temporal characteristics of typical stream communities. For organisms with limited distribution and 

limited capacity to colonize new sites, habitat changes 

at the scale of individual macrohabitats or cross sections can be extremely important. For anadromous 

fishes that migrate between the oceans and far inland, 

the effects of disturbance accumulated over the scale of 

the entire range of movement may need to be assessed. 

For many purposes, the reach scale will be the most 

practical. With the reach as the spatial scale, offsetting 

variations in habitat within the reach would be considered background variation of a system in equilibrium.

In Resh and others (1988), the discussion of the background theory of disturbance in stream ecosystems provides some insight into temporal frames for assessing 

habitat equilibrium. They note that the disturbance 

(departure from an equilibrium condition) is a relatively 

discrete event in time that disrupts ecosystem, community, or population structure and that changes resources, 

availability of substratum, or the physical environment. 

They further state that the frequency and intensity of the 

disturbance event should be beyond a predictable range. 

For example, seasonal changes in habitat availability 

can be quite large in some environments. However, 

because seasonal variation is a predictable cycle of 

repeatable magnitude, stream organisms can adapt to it, 

and seasonality can be considered background variation 

of an equilibrium system. Because of the wide range of 

life histories existing in typical stream ecosystems, the 

time frame for assessing habitat equilibrium probably 

needs to be defined by the life histories of individual 

organisms of concern.

Channel Disturbance and Adjustment

Physical disturbances such as land-use changes, 

instream engineering, and large floods often cause 

changes in channel pattern, cross sectional morphology, 

and bed material (Baker, 1977; Eschner and others, 

1981; Graf and others, 1995; Friedman and others, 

1996), thereby potentially altering habitat characteristics and availability. These changes can occur because 

of changes in the magnitude of physical processes or 

rates of processes, or because a threshold within a fluvial system was exceeded.

Fluvial systems can exhibit lagged, threshold, and 

cumulative responses to imposed disturbances 

(Schumm, 1977). Lagged responses exist because erosion, deposition, and transport of sediment are not 

instantaneous and because sediment tends to travel 

finite distances before being retained temporarily in 

storage. Thresholds exist because of critical shear 

stresses that must be exceeded to transport sediment or 

because of other barriers to geomorphic change that, 

once overcome, produce a nonlinear geomorphic 

response. Disturbances to one part of the fluvial system 

can translate upstream or downstream through the network and diminish or grow in the process, yielding 

complex cumulative responses. At a given site along the 

channel network, therefore, the stream channel can be 

disturbed from activities that occurred at various times 

in the past and at various places elsewhere in the fluvial 

system. This behavior generally is known as “complex 

response” (Schumm, 1977). It may be necessary to 

understand the history of adjustments everywhere 

within the fluvial system to understand fully the effects 

at one particular point within the system.

Fluvial systems can respond to disturbance according to 

several conceptual models (fig. 5). In dynamic equilibrium, channel morphology and stream processes fluctuate around some condition or value (Bull, 1991). The 

acceptable variability in magnitude and frequency of 

the fluctuations depends on factors such as the time 

frame or species of interest. External forcing events, 

such as extremely large floods or land-use changes, may 

cause a stream to transform into a nonequilibrium or 

disturbed state. A change to a nonequilibrium state 

occurs when the event causes erosion and deposition 

processes or rates of processes to change dramatically.
10 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

The general case of disturbance and response consists 

of a forcing event, a response lag, a response, and a 

relaxation period (fig. 5B,C). After the forcing event, 

during the response-lag period, little change occurs in 

either channel form or stream processes. During the 

response period, channel form and stream processes 

react to the external forcing. After the response, the 

channel may relax (recover) to a predisturbance condition at varying rates (fig. 5B), or it may maintain a new 

state (fig. 5C).

The type and extent of land-use disturbances and the 

characteristics of the drainage basin and channel control the magnitude, frequency, spatial extent, 

and persistence of disturbances affecting stream 

habitats. When a basin is temporarily disturbed 

by forest harvest activities, channels may react 

and eventually relax to predisturbance conditions (fig. 5B). On the other hand, a persistent 

change in land use—such as row-crop agriculture or a dam—will have a persistent effect on 

channel forming processes and result in an alternative equilibrium state (fig. 5C). Where the fluvial system response is governed by thresholds, 

even a minor, transient disturbance might have 

persistent effects on channel morphology and 

habitat. An example would be the oversteepening of streambanks with the resultant loss of root 

strength to resist erosion (fig. 6). Once such an 

irreversible threshold is passed, the system may 

remain in the alternative state for substantial 

periods of time (Jacobson and Pugh, 1997).

Habitat Disturbance

Common types of physical disturbances of 

stream habitat can be categorized as those that 

change the habitat volume (for example, by filling pools or widening riffles), those that change 

habitat quality (for example, changing the particle-size distribution of substrate or altering vegetative cover), and those that destabilize 

substrate but leave no net change in either habitat volume or quality (for example, reaches 

where floods transport bedload but leave the 

reach with the same morphology and substrate 

after the flood). These will be referred to as volume, quality, and stability disturbances.

The effects of these different types of disturbances vary 

depending on the life history of individual organisms 

and how they use particular habitats. For example, some 

stream insects may have short life cycles of days to 

months. These organisms will be insensitive to stability 

disturbances if the disturbances are infrequent relative 

to their short life cycles. Conversely, they might be 

quite sensitive to quality disturbances that change the 

particle-size distribution of substrate. A quality disturbance—for example, deposition of fine sediment into 

substrate interstices—could last many macroinvertebrate lifetimes and prevent recolonization.

Figure 5. Types of equilibria, disturbance, and response 

patterns for streams (modified from Bull, 1991). CHANNEL WIDTH

TIME

EXPLANATION

A. Dynamic equilibrium

B. Return to initial 

equilibrium state

C. Change to new

equilibrium state

Transient

Persistent

Forcing

(floods)

Forcing

(floods)

R

R

Equilibrium|–R–L–RX–|Equilibrium

Equilibrium 1|–R–L–RX–|Equilibrium 2

Actual value

Average value

System threshold

Forcing mechanism

Response lag

Response

Relaxation

R–L

R

RX
FACTORS AFFECTING PHYSICAL STREAM HABITAT 11

Other species may require long periods of stable substrate as well as habitat volume and quality. Mussels, 

for example, are long-lived and relatively immobile; 

they depend on stability of the substrate on which they 

live, as well as the habitat quality (Cummings and 

Mayer, 1992; Di Maio and Corkum, 1995). Their 

immobility in adult life stage also limits their ability to 

seek refuge from disturbance or recolonize sites once 

disturbed. Stream fishes, in contrast, may be relatively 

insensitive to stability disturbances because they are 

mobile. If habitat quality or volume is degraded in one 

reach of the stream, they can move and exploit similar 

habitats in other reaches.

Biotic responses to physical disturbance would be 

expected to vary with the persistence, magnitude, and 

frequency of the disturbance. For example, bed scour 

during an individual flood may constitute stability disturbance, but if sediment is redeposited to the original 

channel form during streamflow recession, habitat volume may not be disturbed for a meaningful period of 

time. In contrast, gravel deposited in a riffle during an 

extreme flood may be of sufficient volume to create an 

island with associated persistent changes in benthic 

habitat in the adjacent channels. Because this effect is 

likely to exist until intermediate-sized floods can 

remove the excess gravel, the effect of this habitat-quality disturbance should be measured in part by its persistence through time. Similarly, Wolman and Gerson 

(1978) proposed that the geomorphic effectiveness of a 

flood should be measured in part by the rate of recovery 

of the channel to preflood conditions. A flood that produces persistent morphological changes is considered 

to be more geomorphologically effective and, in many 

cases, would also be more ecologically effective.

Finally, disturbance in either the geomorphic context or 

the ecologic context is not necessarily detrimental. In 

the geomorphic realm, the concept of a reach or fluvial 

system in dynamic equilibrium implies orderly movement of sediment through the system. A disturbed system may be characterized by increased rates of erosion 

or deposition at sites within the system. Usually, accelerated rates of erosion or deposition degrade a valued 

resource. For example, erosion can undermine bridge 

piers or send productive agricultural land downstream; 

excessive deposition can fill a flood-control reservoir. 

However, when geomorphic effects are extended to the 

subject of stream habitat, the value judgment is not as 

clear. For example, accelerated bank erosion may result 

in delivery of large woody debris to the stream ecosystem, thereby creating scour pools, cover, and substrate 

usable by some organisms. Increased disturbance in a 

stream ecosystem may favor a different mix of species 

rather than unequivocal degradation of the biological 

resource. For example, according to the intermediate 

disturbance hypothesis (Resh and others, 1988), 

increased environmental disturbance in some ecosystems can actually increase species richness by displacing some of the habitat-specific species with habitatgeneral, colonizing species. Conversely, too much disturbance can result in subsequent decreases in species 

Water surface Water surface

Ground surface Ground surface

 Convex-upward

bank

Concave-upward

bank

Figure 6. Effect of oversteepening streambanks. Loss of erosion resistance from roots on 

convex-upward banks results in a threshold effect as the bank is steepened to vertical or 

concave-upward. On steep banks, roots no longer provide substantive strength to resist bank 

erosion, resulting in accelerated bank erosion (Jacobson and Pugh, 1997).
The Big Darby Creek Drainage Basin is 

dominated by intense agricultural land

use, and it is bordered on one side by 

expanding suburbs of Columbus, Ohio. 

Despite this destabilizing potential,

Big Darby Creek has maintained

extremely high biological diversity. 

Photograph courtesy of J.A. Hambrook,

U.S. Geological Survey.

Like most streams in the Midwestern United States, Big Darby Creek in 

Ohio has been affected by widespread, intensive row-crop agriculture. 

In addition, the eastern margin of Big Darby Creek Basin is being 

affected by urban expansion of the Columbus, Ohio, metropolitan 

area. These sources of potential land-use disturbance have motivated 

studies of Big Darby Creek by the USGS in cooperation with the city of 

Columbus, Ohio, and Franklin, Madison, and Pickaway Counties. The USGS 

study has been coordinated with a unique partnership of public agencies and 

private landowners—The Darby Partners—that has recognized the need to develop a 

rigorous scientific basis for management of aquatic resources.

Despite the history of intensive agricultural land use, Big Darby Creek supports diverse and abundant fauna, 

including 86 species of fish and 40 species of freshwater mussels. Because of these qualities, Big Darby has been 

designated a “State Scenic River” by the Ohio Department of Natural Resources, a “National Scenic River” by the 

U.S. Department of the Interior, and a “Last Great Place” by The Nature Conservancy. The threat of increased 

urbanization with potential for increased peak flows and associated increases in loads of nonpoint-source 

contaminants prompted a detailed field study to evaluate present-day effects of disturbance on the habitat and 

benthic communities.

The study objectives were to (1) document suspended-sediment and water-quality characteristics of the drainage 

basin; (2) quantify benthic habitat disturbance; (3) measure the washout of streambed substrate and 

recolonization by macroinvertebrates and algae; and (4) relate physical disturbance factors to washout and 

recolonization rates. The understanding of disturbance and recovery processes gained from this study provide a 

foundation for predicting future changes to benthic communities as hydrology and sediment supply are altered.

The study design was based on pre- and postflood characterization of bed material, macroinvertebrates, and algal 

communities. The results of two monitored floods demonstrated that the floods substantially changed bedmaterial particle-size distributions and decreased macroinvertebrate and algal-cell densities. However, the 

magnitudes of the floods and the biological responses were poorly correlated. The investigators indicated that the 

temporal adjustment of the macroinvertebrate community was affected by time lags and biotic factors such as 

life-stage history. For example, a decrease in Diptera (true flies) densities in July probably was related to 

emergence from larval to adult life stage, not to disturbance by a preceding flood. The investigators also—

Map

Area

OHIO

L a k e Eri e

Big Darby Creek

Columbus

OHIO

0

0 50 MILES

50 KILOMETERS

Hydrologic Disturbance in an Agricultural-Urban Basin—

Big Darby Creek, Ohio

12
determined that the sensitivity of macroinvertebrates to disturbance varied with season and flow-exposure group 

(that is, groups of macroinvertebrates characterized by the way in which body shape is adapted to specific flow 

conditions). Algal responses to disturbance similarly were complicated by form. Mat-forming blue-green algae 

appeared to be less sensitive to disturbance than stalked species. Moreover, recolonization of algal communities 

appeared to be a complex function of disturbance magnitude, water temperature, canopy conditions, initial 

density of algal cells, and grazing by fish and invertebrates. Because the study characterized both physical and 

biological components of flood disturbance in detail, it provides understanding necessary to link habitat changes 

with biological responses. For the moderate floods monitored, changes in physical habitat were documented by 

changes in bed-material particle size. The biological response to this moderate disturbance was measurable but 

complex. The implication of these complexities is that expected increases in magnitude and frequency of 

disturbances will have substantial but relatively unpredictable effects on the benthic community of Big Darby 

Creek.

For more information, refer to Allan (1991), Hambrook and others (1997), Mihaly (1994), and Palcsak (1995).

13

The U.S. Geological Survey and the Darby 

Creek Partners have been studying the 

effects of hydrologic disturbance and 

sediment yield on algal population and 

benthic invertebrates in Big Darby Creek 

Here, U.S. Geological Survey hydrologists 

employ a freeze-core sampling device to 

obtain undisturbed samples of bed material 

for analysis. Photograph courtesy of J.A. 

Hambrook, U.S. Geological Survey.
14 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

richness if communities become dominated by colonizers. The maximum richness occurs at intermediate levels of disturbance that can accommodate some of both 

habitat-specific and colonizing species. In another 

example of the potential value of disturbance, unstable 

reaches of streams in the Ozarks (southern Missouri and 

northern Arkansas) have some of the most productive 

marginal habitats for primary productivity, organic matter cycling, and rearing of young fish (C.F. Rabeni, U.S. 

Geological Survey, oral commun., 1997).

Land-Use Induced Disturbances of Physical Stream 

Habitat 

Both upland and riparian land-use changes can cause 

habitat disturbances by altering the amount and timing 

of runoff and sediment yield in streams (table 1). Runoff is that portion of rainfall that falls to earth and runs 

off the ground surface rather than infiltrating into the 

soil or evaporating. Sediment yield is the quantity of 

eroded material that is discharged from above a point in 

a drainage basin. Upland land-use changes are considered to be those that occur on slopes and ridges at elevations above the flood plain. Riparian land-use 

changes generally refer to changes occurring from the 

margin of the low-water channel up to and including the 

flood plain.

Upland and riparian land-use changes can occur over a 

short period, or they can be persistent. They may be 

restricted to a small area or occur throughout a drainage 

basin. For example, effects of agricultural land clearing 

generally persist for decades or more, causing a persistent, widespread disturbance. In contrast, instream 

gravel mining to build a local road may cause a shortterm point disturbance directly in the channel. The location, type, persistence, and propagation of a disturbance 

determine the severity of the effect on the physical habitat of the stream.

Upland Land-Use Changes

Upland land-use changes, such as deforestation, reforestation, and urbanization, often alter rainfall-runoff 

relations, thereby changing the hydrologic budget of a 

stream. Many land-use changes increase runoff by 

decreasing infiltration rates, evapotranspiration, or permeable area. Increases of impermeable area in urbanized basins typically result in substantial and welldocumented increases in peak discharges (Haan and 

others, 1994). Generally, channel area increases (fig. 7) 

to accommodate the increased discharge, leading to 

channel deepening or widening, or both (Booth, 1990).

Increased runoff from land-use practices in rural areas 

can be more subtle and difficult to document, especially 

for drainage basins greater than about 5 square kilometers in area (Potter, 1991; Jones and Grant, 1996). In 

addition, hydrologic effects of land clearing and forestry (fig. 8) can be subject to rapid recovery if vegetaFigure 7. Hydrologic changes due to 

urbanization in a drainage basin can have 

severe effects on stream habitat. Increased 

impermeable area in urbanized drainage 

basins typically yields greater storm runoff, 

higher peak flows, and diminished base flows. 

In this example from St. Louis County, 

Missouri, increased peak flows have resulted 

in substantial widening, incision, and 

instability of stream channels. Loss of habitat 

is complete because of loss of base flow; 

before urbanization, this stream supported 

perennial flow and diverse aquatic habitat.
FACTORS AFFECTING PHYSICAL STREAM HABITAT 15

tion is allowed to regrow (for example, Hornbeck, 

1975). An illustration of the subtle effect of rural land 

use on storm runoff is shown in figure 9. Here, the percentage of rainfall that runs off the landscape is shown 

as calculated from a curve-number method (Soil Conservation Service, 1972) for two storm durations, two 

soil groups, and a range of land-use practices. For a 1-

inch, 24-hour rainfall, the percentage of rainfall becoming runoff ranges from 69 to 95 percent, and for a 4-

inch, 24-hour rainfall, the percentage ranges only from 

91 to 98 percent. Land use has a relatively minor effect 

on runoff for the more intense storm events that would 

be expected to create flows capable of rearranging 

channel habitat.

The effects of rural land-use change on channel morphology and habitat can be more difficult to discern 

than the effects of urban land use. For example, Costa 

(1975) noted that streams on the Maryland Piedmont 

that had been affected by agricultural runoff had greater 

Figure 8. Upland land-use processes in rural 

areas can decrease infiltration, increase runoff, 

and increase soil erosion. Typical land-clearing 

practices in the Ozarks of Arkansas have the 

potential to increase peak flows moderately until 

grasses are reestablished. The effect of increased 

sediment yield from such clearing can be severe. 

In this case, sediment yield is minimized by 

storage of organic debris in the axis of the 

unchanneled valley. However, sediment 

accumulations in the organic debris may be 

delivered to streams years in the future as the 

organic debris decomposes.

Figure 9. Predicted percentage of rainfall becoming runoff estimated from the Soil 

Conservation Service (1972) curve number method for typical rural land uses. If all other 

factors are constant, changes in land use create variations in runoff. The B and C soil 

hydrologic groups are for soils with moderate infiltration and storage characteristics. For 

low-intensity rainfall (1 inch in 24 hours), the most severe land-use practice will produce as 

much as 25 percent greater runoff than the least intrusive land-use practice. For more 

intense rainfall (4 inches in 24 hours), comparable to the intensity necessary to generate a 

channel-forming flow, runoff is relatively insensitive to land use.

60

65

70

75

80

85

90

95

1-INCH, B SOIL

1-INCH, C SOIL

4-INCH, B SOIL

4-INCH, C SOIL

Dirt

road

Fallow Row

crop

Grain Pasture Meadow Wooded

EXPLANATION

100

PREDICTED PERCENTAGE OF RAINFALL 

BECOMING RUNOFF

LAND USE
North Fish Creek near Ashland, Wisconsin, 1994. North Fish Creek near Ashland, Wisconsin, 1996.

Historical information was used to investigate links between 

land-use changes and channel changes in a small basin on the 

shore of Lake Superior, northern Wisconsin (Fitzpatrick and 

others, 1999). Excessive degradation and aggradation of 

stream channels has been thought to contribute to degradation 

of spawning habitat for steelhead, coho salmon, and trout, and 

also may be affecting coastal wetlands. A study by the USGS in 

cooperation with the Wisconsin Department of Natural Resources 

evaluated long-term changes in sediment loads, changes in channel 

morphology, and links to land-use practices. North Fish Creek was selected for the 

study because it has one of the largest anadromous fish populations in the State and 

because information gathered on North Fish Creek should apply to many other tributary basins to Lake Superior.

North Fish Creek is a small creek (drainage area 122 square kilometers) that drains into the Chequamegon Bay of 

Lake Superior. Despite its small size, the physiography of North Fish Creek varies considerably from upstream to 

downstream. The upper reach (river kilometer 19 to 27) has a steep channel gradient, narrow flood plain, and 

valley walls with large, highly erosive bluffs. The channel bed substrate is composed of boulder, cobble, gravel, 

and sand. The middle reach (river kilometer 13 to 19) has a transitional channel gradient and widening flood plain. 

The channel bed substrate is gravel to mostly sand with occasional gravel. This reach is characterized by mass 

wasting of the stream banks and an unstable channel. The lower reach (river kilometer 0 to 13) has a flat channel 

gradient and a wide flood plain. The channel bed substrate is sand with minor gravel. Few eroding bluffs are in 

this reach because the flood plain is wide enough to accommodate the meandering pattern of the stream. Banks 

are stable and vegetated, but subject to accelerated sedimentation from floods.

The drainage for North Fish Creek is geologically young, having been formed by incision into glacial deposits 

during the last 9,000 years. Ongoing geomorphic responses to incision and isostatic adjustments create 

complications for separating natural geomorphic changes from human-induced changes. For example, excessive 

sedimentation in the downstream reaches may be controlled in part by relative downward isostatic adjustment of 

the land surface and in part by land-use induced increases in sediment supply. Moreover, like most landscapes, 

North Fish Creek is affected by highly variable hydroclimatic events that obscure direct links to land-use changes.

Channel incision in the upper reaches of Fish Creek apparently has resulted in accelerated streambank 

erosion and delivery of sediment directly to the channel. Photographs courtesy of F.A. Fitzpatrick, U.S. 

Geological Survey.

Map Area

WISCONSIN

NFishCk

Superior

Lake

Chequamegon Bay

Ashland

WISCONSIN

MINN

MICH

0

0 50 MILES

50 KILOMETERS

Geomorphic Instability and Sediment Loads—Wisconsin

16 
The excessive sedimentation in the lower reaches of North Fish Creek is thought to have started with land-use 

changes beginning in the late 1870’s. During European settlement approximately 125 years ago, the forest lands 

were cleared by logging and burning and converted to farm lands. Currently (2000), the land use is a mixture of 

pasture, hay fields, and immature forest that commonly is harvested for pulp wood.

A stratigraphic approach was used to characterize presettlement variability in sedimentation rates and processes 

and to evaluate the magnitude of change associated with post-European land-use changes. Sediment cores from 

relict channels were used to identify the original size, shape, and sediment texture of these channels. Also, 25 

stream banks and bluff exposures were examined to assess presettlement and historical sedimentation rates and 

to assist with the interpretation of long-term changes in the drainage system. The sedimentation rate in the lower 

reach has been episodic during both pre- and postsettlement time, although large sedimentation events have 

become more common in postsettlement time. A single large flood in 1946 caused the most sedimentation and 

channel change since European settlement. Both the amount and texture of sediment deposits have changed after 

European settlement and have continued to change during the last 100 years. The postsettlement sediment 

deposits are coarser than those of presettlement, and most of the recent sediment load appears to have 

originated from 17 large eroding bluffs located in the middle and upper reaches.

Modern and historical stream channels were compared where landsurvey section lines cross North Fish Creek from the mouth to river 

kilometer 27. Historical channel dimensions and substrate characteristics 

were obtained from a Government Land Office survey of the area done 

during 1855. The resurveys indicate that in the upper and middle 

reaches the channel eroded vertically 1 to 3 meters during the last 125 

years. The stream channel has narrowed and incised, resulting in a 

channel that can accommodate larger flows than the channel that 

existed in 1855. Confinement of the flow to the narrow channel is 

thought to result in increased potential to erode stream banks and the 

channel bed. This type of channel is efficient at rapidly transporting 

sediment and water downstream. Pre- and postsettlement channel bed 

substrates were similar. Surveys at 6 of 17 large bluffs in the upper and 

middle reaches have shown retreat magnitudes of 0 to 28 meters, with 

an average retreat of 16 meters, during 52 years. 

In contrast to the incision and erosion documented in the upper and 

middle reaches, the stream channel of the lower reach has aggraded by 

as much as 2 meters and has widened during the last 140 years. Lower 

stream banks enable sediment-laden flows to spill easily into the wide 

flood plain and deposit the sediment load. The sediment load is 

estimated to be almost 10 times greater today than in presettlement 

times. Both the channel and flood plain have aggraded 1 to 2 meters in 

this reach during the last 140 years.

Historical analyses of the links between land-use and habitat changes on 

North Fish Creek provide information that may be important for future 

resource-management decisions. The historical data show the spatial 

link between erosion at discrete points in upstream reaches and 

sedimentation in downstream reaches, thus showing resource managers 

where restoration efforts would be most effective. These data also 

document the presettlement reference condition and show how 

instream and riparian habitats are likely to change in response to 

extreme hydroclimatic events.

For more information contact Faith Fitzpatrick, U.S. Geological Survey - 

Water Resources Division, 8505 Research Way, Middleton, WI 53562 

phone: 608-821-3818 email: fafitzpa@usgs.gov 

Vibracoring of sediments of Fish 

Creek provides evidence for 

changes in stream energy and 

sediment yield over hundreds to 

thousands of years. These data 

help determine the natural 

background of channel changes 

for comparison to channel 

changes suspected to have 

resulted from land-use changes. 

Photograph courtesy of F.A. 

Fitzpatrick, U.S. Geological 

Survey.

17
18 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

recurrence intervals for bankfull flows for drainage 

basins smaller than 26 square kilometers than for drainage basins greater than 26 square kilometers. Costa 

(l975) and Jacobson and Coleman (1986) interpreted 

these data to indicate that smaller streams had 

entrenched, in part due to increased runoff from agricultural land use. Channels also may narrow as a result of 

basinwide recovery from land-use changes. For example, Buttle (1995) documented channel narrowing and 

decreased width-to-depth ratios following reforestation 

and consequent reduction of peak flows in the headwaters of the Ganaraska River in Canada.

The net result of upland land-use practices on channels 

and stream habitat also is greatly affected by sediment 

yield, and in many cases runoff and sediment yield both 

change with land-use changes (fig. 10). Increases in the 

sediment yield from the basin to the stream often result 

from loss or change of vegetative cover, increases in 

roads, or increases in gullies (Trimble, 1974; Reid and 

Dunne, 1984; Waters, 1995). Generally, for a given 

upland land-use change, the relative increase in soil erosion on slopes is many times greater than the increase in 

storm runoff. This is illustrated with a comparison of 

cover factors from the Universal Soil Loss Equation 

(USLE) (Wischmeier and Smith, 1978). If all other factors on a slope are held constant except for land-use 

change as depicted by the cover factor variable, soil erosion will be proportional to the cover factor. For the 

range of land-use types shown in figure 11, soil erosion 

is predicted to be as much as 1,000 times greater than 

the natural background rate (that is, compared to natural 

woodland or natural grassland). By comparison with 

figure 9, it can be seen that the potential relative effect 

of land-use change on sediment yield typically is much 

greater than that of runoff.

Realization of the soil-erosion potential requires that 

eroded soil is delivered from slopes to stream channels. 

However, sediment can move slowly from slopes to the 

channel and downstream as it is episodically deposited, 

stored, and remobilized. Therefore, sediment yield is 

can be substantially less than predicted by soil erosion 

models and yield is expected to lag behind the disturbance.

Increased sediment yield to streams generally results in 

channel aggradation or changes in bed material grain 

sizes, or both (Schumm, 1977). A common result of 

increased upland sediment yields is increased deposition of fine sediment (silt and clay) with potential 

decreases in pool volume, increases in substrate embeddedness, and decreases in interparticle pore space in 

gravel used for spawning (for example, Lisle and Hilton, 1992; Madej, 1995). In some cases, aggradation 

also can be expected to lead to increased channel instability and habitat disturbance. A comprehensive review 

of the effects of sedimentation on stream habitats is presented by Waters (1995).

Some types of land-use change—or recovery from previous disturbance—can result in decreased sediment 

yield. Decreases in sediment yield may result from 

increased vegetative cover or artificial barriers to erosion, such as retaining walls and asphalt cover (Arnold 

and others, 1982; Buttle, 1995). Decreased sediment 

Figure 10. Landslides develop on intensely 

grazed slopes such as those in the Appalachian 

Mountains of West Virginia. Increased 

frequency of shallow landslides like these has 

been associated with conversion of woodland 

to grassland (Jacobson, 1993). These landslides 

deliver sediment directly to the stream channel.
FACTORS AFFECTING PHYSICAL STREAM HABITAT 19

yield can cause channel degradation or widening (Jacobson and Coleman, 1986) and coarsening of bed material (Dietrich and others, 

1989).

Because water and sediment move downstream 

in a branched network, the effects may be 

cumulative downstream. A key question is 

whether sediment from disturbances travels 

downstream as coherent waves or spreads out 

longitudinally along the stream channel (for 

example, studies by Meade, 1985; James, 

1993; Madej, 1995). In the former case, waves 

that meet and grow in the channel network 

would be expected to create substantial downstream cumulative effects. In the latter case, 

sediment effects would be expected to diminish downstream.

The timing and sequence of hydrologic and 

sediment yield changes can result in extreme 

changes in channel morphology and habitat 

availability. An example is the typical model of channel 

responses to a cycle of urbanization (Arnold and others, 

1982). In the Sawmill Brook Basin, Connecticut, runoff 

and sediment yield initially increased in response to 

urbanization. Then, as construction waned and land surfaces were stabilized, sediment yield decreased while 

storm runoff remained substantially elevated relative to 

nonurban conditions. Decreased sediment yield coupled with increased runoff led to loss of coarse bed 

material in the downstream portion of the basin and 

consequent channel incision (Arnold and others, 1982). 

In a contrasting example, Odemerho (1992) noted that 

extreme urbanization in a tropical landscape in Nigeria 

resulted in channel narrowing and aggradation because 

the increases in sediment yield were much greater than 

simultaneous increases in runoff and sediment transport 

capacity.

Riparian Land-Use Changes

Similar to upland land-use changes, some riparian landuse changes (for example, impoundments and outfalls) 

also can alter water discharges and sediment yield (fig. 

12). Other riparian land uses can alter hydraulic resistance, erosion resistance, or energy of a channel without 

changes in hydrologic and sediment budgets 

being imposed (fig. 13). Because riparian landuse changes affect the channel directly or nearly 

directly, the effects on channel morphology and 

stream habitat often are directly manifest and 

clearly discerned.

Figure 12. Dams and reservoirs directly affect 

stream habitat by controlling quantity and 

timing of water discharge and by decreasing 

sediment yield to downstream channel 

segments—Gavins Point Dam, Missouri River, 

near Yankton, South Dakota.

SOIL EROSION RATIO

1,000

100

10

1

0.1

Dirt road Bare soil Grazed Natural

grassland

Natural

woods

LAND USE

Figure 11. Predicted ratio of soil erosion from specified land-use 

classes to soil erosion from natural woodland. These ratios are 

calculated from Universal Soil Loss Equation (Wischmeier and 

Smith, 1978) cover factors for typical rural land-use types. If all 

other factors—slope, rainfall intensity, soil properties—are 

constant, soil erosion increases with the cover factor. Hence, 

inherent soil erosion potential can be quantified as a ratio to the 

least severe land-use class. Note that the ratios are on a 

logarithmic scale.
Surface- and ground-water withdrawals in a drainage basin may have 

substantial effects on river flood-plain 

ecosystems, even in the humid coastal 

plain of the southeastern United States. 

The USGS, in cooperation with the Northwest 

Florida Water Management District, recently 

completed a study of the effects of increased water 

withdrawals on aquatic habitats in the flood plain of 

the Apalachicola River. A previous USGS study, in 

cooperation with the Florida Game and Fresh Water 

Fish Commission, investigated the use of flood-plain 

habitats by fish in the Ochlockonee River. These studies have 

been designed to develop a more complete understanding 

of how flood-plain ecosystems function on low-gradient, coastal-plain 

streams; define ecological reference conditions to assess the affects of 

changing hydrology; and quantify the volumes and durations of aquatic 

flood-plain habitat under natural and regulated conditions.

North Florida coastal-plain rivers wind slowly through densely-forested floodplains. Although some parts of the 

flood plain are as much as 4.6 meters above low water in the adjacent river channel, the entire flood plain 

generally is inundated with flowing water each year during the annual flood. Some parts of the flood plain are 

submerged for only a few weeks, whereas others are submerged for nearly one-half of the year because of 

differences in flood-plain elevations. Flood-plain depressions are vegetated with tupelo and cypress trees and 

often contain water that is isolated from the main channel. Many streams and lakes in the flood plain are 

alternately connected to and disconnected from the main channel as river levels fluctuate. Increased withdrawals 

or flow regulation can decrease the amount of flood-plain habitat accessible to main-channel fishes. Decreases in 

flood-plain flooding duration can also alter the flood-plain vegetation community.

Approximately three-fourths of known main-channel fish species were collected in the flood plain of the 

Ochlockonee River during floods. The diversity of fish species in the flood plain indicates that flood-plain habitats 

probably play a crucial role in the life cycle of many main-channel fish. Fishes in inundated forested flood plains 

have access to abundant supplies of food, spawning sites (many species have eggs that adhere to wood), and 

refuges for young and nesting fish. Altering the season or magnitude of the annual flood could substantially 

restrict the use of flood-plain habitats by these fish species. In ponded habitats on the flood plain, the diversity of 

fish species tends to decrease dramatically as pond area decreases. Dwindling habitat size, caused by droughts or 

water withdrawals, could decrease the diversity of fish species, with the greatest effect on those species that are 

restricted to the flood plain.

For more information refer to Leitman and others (1991) and Light and others (1998).

Map Area

FLORIDA

Apalachicola R

Ochlocknee River

Gulf of Mexico

 Lake

Seminole

Tallahassee

FLORIDA

ALABAMA GEORGIA

0 25 KILOMETERS

0 25 MILES

Water Withdrawals and Maintenance of Flood-Plain 

Ecosystems—Florida

20
Studies that link forest habitat and fish 

habitat availability to river levels are an 

important tool that water managers can 

use to assess the effects of water use on 

flood-plain ecosystems. Areas of higher 

elevation support bottomland forests of 

spruce pine, sweet gum, live and water 

oak, and the lower elevations support a 

cypress/tupelo forest community.

North Florida coastal-plain rivers wind 

slowly through densely forested flood 

plains. The diversity of fish species in the 

flooded plain indicates that these habitats 

probably are crucial in the life cycle of 

many main-channel fish. Studies have 

quantified the link between channel 

hydrology and availability of flood-plain 

aquatic habitats. The link is essential for 

evaluating the ecological effects of 

alternative water-withdrawal decisions.

21
22 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

Water impoundments and diversions can alter the timing and amount of water in a stream, as well as changing channel morphology. Reviews of the geomorphic 

and ecologic effects of reservoirs can be found in Williams and Wolman (1984), Ligon and others (1995), and 

Collier and others (1997). Direct effects of regulation 

by reservoirs often are transmitted as changes in 

streamflow, water temperature, and sediment-related 

turbidity. Regulation for multiple purposes such as 

flood control, power generation, and navigation usually 

changes flow characteristics, which in turn change the 

seasonal distribution of depths, velocities, temperatures, and turbidity that are available to organisms. In 

particular, regulation that disrupts an annual flood pulse 

(Junk and others, 1989; Bayley, 1995) has been implicated in the decline of native species. Seasonal temperature changes can directly affect fish energetics and 

disrupt temperature-related spawning cues (Hesse and 

Sheets, 1993). On the other hand, consistent, low-temperature discharge from reservoirs also can support substantial coldwater fisheries. Decreases in turbidity due 

to sediment trapping by dams also can result in a competitive advantage for sight-feeding nonnative fishes 

relative to species that have evolved to compete in highturbidity environments.

Geomorphic changes as a result of regulation can 

include channel simplification, incision, disconnection 

of side-channel and flood-plain water bodies, and bedmaterial coarsening. Investigations of morphological 

and sedimentological changes due to river regulation 

have shown that effects can extend tens to hundreds of 

kilometers downstream (Williams and Wolman, 1984). 

Regulation typically involves decreases in peak flows, 

resulting in decreases in flows that transport sediment 

and maintain in-channel habitats. Decreases in peak 

flows and sediment-transporting events often lead to 

encroachment of vegetation, which increases the stability of sediment and, thereby, causes channel narrowing 

and island growth and attachment to the flood plain 

(Graf, 1978; Freidman and others, 1996; Scott and others, 1996). Increased stability of the channel under regulated conditions may result in the disappearance of 

habitats formerly maintained by disturbance—for 

example, unvegetated sandbars. In addition, loss of sediment load due to trapping of sediment in the reservoir 

B, Dense riparian vegetation and nearly closed 

canopy about 3 kilometers downstream of area 

shown in A. The location of Little Piney Creek is 

shown in the section “Establishing Land-Use History 

and Habitat Links—Missouri” on p. 32.

Figure 13. Aggregate mining in stream channels or in riparian zones can affect stream habitats directly.

A, Flood-plain aggregate mining pits, Little Piney

Creek Missouri. Although this process is not

directly in the stream channel, the stream habitat

has been degraded by straightening the channel

and removing all riparian canopy, thereby reducing hydraulic diversity, shading, cover, and

organic input. Moreover, the buffers between the

channel and the pits cannot be expected to

remain intact as natural stream migration takes

place (compare with map of channel migration

for this same stream, fig. 3).
FACTORS AFFECTING PHYSICAL STREAM HABITAT 23

can result in channel incision disconnecting the channel 

from the flood plain and side channels. Loss of fine sediment typically results in coarsening of the streambed 

sediment in tailwater (downstream) segments of the 

river, potentially resulting in changes in spawning habitat and decreasing the ability of some benthic organisms to burrow into the bed (Donnelly, 1993).

In contrast to the case of sediment starvation below 

dams, mining effluent can introduce large quantities of 

sediment directly to the channel or riparian zone (Gilbert, 1917; Lewin and others, 1983; Marron, 1992; 

James, 1994; Waters, 1995). Large volumes of miningrelated sediment can aggrade channels, fill pools, and 

choke channel substrates with fine sediment. Excessive 

sediment also can cause channels to steepen, with consequent increases in braiding, sinuosity, migration 

rates, and disturbance.

Channel engineering directly alters physical stream 

habitat (fig. 14). Generally, instream engineering such 

as channelization, levees, and navigation structures substantially decreases the surface area of the channel, 

thereby decreasing shallow-water habitat area (Gore 

and Shields, 1995). In addition, these types of engineering projects generally decrease habitat diversity by 

decreasing the range of available depths and velocities. 

Channelization can have particularly severe and persistent effects on channel morphology by increasing channel slopes while decreasing hydraulic roughness. The 

net result in many areas is channel incision and widening, with increases in solar radiation and decreases in 

organic contributions from riparian vegetation. The processes of disturbance by channelization and subsequent 

channel recovery have been described by Hupp and 

Simon (1991), Simon and Hupp (1992), and Simon 

(1994).

Levees constrict flows at high discharges, thereby 

increasing channel energy and isolating the channel 

from its flood plain. Constricted flows from levees and 

navigation structures have been implicated in exacerbating channel incision and in increasing flood stages 

(Belt, 1975). Disconnecting channels from flood plains 

decreases water and sediment storage on flood plains, 

preventing exchanges of organic material and nutrients 

between the channel and the flood plain, and decreasing 

spawning and rearing habitat for many fishes. Levees 

often contribute to the disruption of the flood pulse on 

regulated rivers (Junk and others, 1989; Bayley, 1995). 

Bank revetments and wing dams or spurs intended to 

stabilize and maintain navigation channels can have 

complex functions in altering habitat. Revetments that 

close off side channels and off-channel habitats from 

the main flow decrease the diversity of habitat available 

to stream organisms. Wing dams (fig. 15) focus the flow 

to maintain depth and scour in a navigation channel, but 

have the added effect of adding a diverse mixture of 

depth and velocity on the landward side. The habitats 

created by such navigation structures are not natural to 

most navigable rivers, but they may be useful for many 

organisms. Structures can be designed to optimize engiFigure 14. Channelization has resulted in a 

deeply incised stream channel on Cane 

Creek, western Tennessee. This is a typical 

Mississippi Lowland physiographic region 

stream that has been subject to channelization to improve land drainage. In 

response to the increased gradient, the 

channel incises, which subsequently destabilizes the stream banks, beginning a 

process of recovery that may take 50 years 

to complete (Simon and Hupp, 1992). The 

location of Cane Creek is shown in the 

section “Habitat in Channelized 

Streams—Tennessee” on p. 24. Photograph 

courtesy of C.R. Hupp, U.S. Geological 

Survey.
Streams of the low, wet ground of the Mississippi 

Embayment have been subjected to extensive 

straightening and channelization to drain land 

for cultivation. The geomorphic and botanical 

effects of this direct land-use change in west Tennessee stream 

channels have been the subject of extensive study by the USGS 

in cooperation with the Tennessee Department of Transportation. 

Recently, study of channelized west Tennessee streams has expanded to 

include consideration of how riparian vegetation functions in the addition, 

transport, and processing of organic materials in these highly disturbed streams. 

This recent work was part of a cooperative interagency effort among the USGS, the 

U.S. Department of Agriculture–Natural Resources Conservation Service, the Shelby County (Tennessee) Soil and 

Water Conservation District, and the University of Memphis Geography Department.

Historical analysis of stream responses to channelization identified a six-stage process (Simon and Hupp, 1992). In 

this sequence, construction is followed by degradation, bank instability, and channel widening. After several 

decades, the channel recovers through flattening and revegetation of the banks and deposition of point and lateral 

bars on the channel margins. Physical channel and bank recovery is accompanied by systematic vegetative recovery 

in the riparian zone. Vegetation on the banks also increases bank stability. Although studies of channel instability in 

west Tennessee focused on channel adjustments and riparian vegetation, changes to instream habitat can be 

inferred. Immediately following the construction phase, channels would be expected to be wide and shallow with no 

woody debris and little hydraulic diversity or canopy cover. With increased gradient, bed scour and habitat 

disturbance would be frequent; at this stage, bank failures can reintroduce large, woody debris into the channel and 

there by enhance scour habitat. As banks stabilize and the channel begins to meander between lateral bars within 

the constructed banks, the low-flow channel would be expected to narrow and form riffle-pool sequences. Finally, as 

woody vegetation recovers on the banks, shading, cover, and organic matter would increase. Studies on stream 

habitat in channelized streams in northwest Mississippi confirm these associations (Shields and others, 1994).

The effects of riparian vegetation on biological structure and organic processing functions of channelized streams 

were studied in detail on a first-order segment of Beaver Creek in southwestern Tennessee. Beaver Creek is a 

channelized stream that is located in a basin dominated by agricultural land use. The creek is 4.02 kilometer in 

length and primarily is a pool/riffle stream type during base-flow conditions. The creek drains a 2.02-square 

kilometer area that predominately is in row-crop cultivation.

The study was designed to evaluate biological functions of the creek as an indicator of stream health and water 

quality. The ability of a stream to process organic material for use as an energy source is one indicator of stream 

health. Modification of streams may disrupt additions, transportation, and processing of organic matter, either by 

directly changing organic matter additions from riparian vegetation or by changing the instream habitat in which 

processing organisms live. Particulate organic matter is the base of the food chain, feeding stream invertebrates 

which, in turn, feed higher trophic levels.

herbaceous riparian vegetation and a 1-kilometer downstream reach of woody riparian vegetation. The reach with 

herbaceous riparian vegetation was shallower and wider than the woody reach, and the banks were actively eroding 

by mass wasting processes. The banks of the reach with woody riparian cover appeared to be more stable; however, 

the streambed of the woody reach was observed to be mobile during 17 weeks of observation. Five pools were 

sampled in each reach and one pool was sampled in the transitional zone between the two reaches.

The biological structure was assessed by collecting macroinvertebrate samples by grab and leaf-pack methods in 

each pool. Both types of samples were collected 36, 66, and 116 days after the leaf packs were deployed. The leaf 

packs were weighed before and after deployment. The net change in dry weight was recorded and used as a 

measure of decomposition or processing function. Invertebrates in the leaf packs were identified and counted to 

determine population characteristics. Temperature, specific conductance, pH, dissolved oxygen, alkalinity, and 

turbidity were measured weekly at the sites.

The herbaceous reach generally had greater variability and range in the chemical measurements than the woody 

reach. The number of macroinvertebrates were greater in the herbaceous reach than in the woody reach, but the 

Map Area

TENNESSEE

0 50 KILOMETERS

0 50 MILES

TENNESSEE

ARK

Memphis

Beaver

Creek

Cane

Creek

Cold

Creek

Habitat in Channelized Streams—Tennessee

24
population of invertebrates (measured in terms of abundance and diversity) in the woody reach was more stable. 

Leaf weight loss indicated that the material was decomposed (processed) in the herbaceous reach at a rate 45 

percent greater than that in the woody reach. The higher rate of decomposition could be because the herbaceous 

reach, which had less shading, had higher water temperatures, which stimulates faster rates of processing and a 

greater number of macroinvertebrates.

The study results demonstrate the substantial effect that riparian vegetation can have on organic processing and 

invertebrate populations in these disturbed streams. Increased rates of organic processing in herbaceous reaches 

may affect downstream reaches by decreasing export of energy sources. Increased fluctuations of invertebrate 

populations in herbaceous reaches also might be expected to affect population fluctuations among fish that feed on 

invertebrates. Byl and others (1996) indicated that differences in bank and bed stability between the herbaceous and 

woody reaches probably were an additional interdependent factor determining biological functions of the stream.

For more information refer to Byl and Carney (1996), Byl and Hutson (1996), Diehl (1994), Diehl (1997), Doily and 

Baker (1995), Petersen and Petersen (1991), Shields and others (1994), and Simon and Hupp (1992).

Channelized streams in the Mississippi Embayment of western Tennessee typically undergo a multiple-stage 

process of channel evolution from disturbance to recovery (Simon and Hupp, 1992). This evolution creates 

dynamic habitat changes, with substantial changes to depth, width, and canopy closure (photos A–D). 

Photographs courtesy of T.D. Byl, U.S. Geological Survey.

A, Beaver Creek, an unchannelized reach with stable 

banks, meandering channel, and a closed canopy.

B, Beaver Creek, a channelized reach with open 

canopy and a straight channel.

C, Cane Creek, a channelized, incised reach with unstable, slumping banks, high sediment yield to 

streams, and no canopy.

D, Cold Creek, in the recovery stage in which the formerly incised channel is aggraded by sediment from 

upstream. In this reach riparian, woody vegetation is 

becoming established, but excessive sand deposition 

has clogged the channel.

25
ELEVATION, IN METERS 

AABOVE ARBITRARY DATUM

DISTANCE ALONG TRANSECT IN METERS 

VERTICAL EXAGGERATION X 12

Ineffective 

bank 

vegetation

Vegetation bands 

on gravel bar

93

94

95

96

97

98

99

100

-20 0 20 40 60 80 100 120

March 1991 

May 1992

March 1993 

December 1993 

March 1995 

February 1997

Riparian vegetation often is cleared for 

flood-control or agricultural purposes. 

Because vegetation increases flow 

resistance by as much as an order of 

magnitude, vegetation removal can 

substantially affect channel shape and 

stream habitats. In cooperation with 

the Missouri Department of Conservation, 

the USGS has been studying the effects of 

woody riparian vegetation on stream 

habitats in the Ozarks (Missouri and 

Arkansas). These studies show vegetation 

substantially affects the type and diversity 

of habitats in many stream reaches.

An abundance of aquatic species live in the clear, spring-fed 

streams of the Ozarks. More than 100 fish species live in Ozarks 

streams—56 fish species and subspecies are restricted to the Ozarks. 

This rich natural heritage may be threatened because erosion and 

deposition, which can result from removal of riparian vegetation, 

continually alter stream habitats.

Study results indicate that flow resistance contributed by vegetation is most effective in areas where gravel 

deposition is occurring. Willows and sycamores often sprout on gravel bars in bands parallel to the stream. Dense 

vegetation bands on gravel bars increase flow resistance and trap sand and gravel during floods. The sand and 

gravel trapped in the vegetation band confines the stream, resulting in local deepening of the channel and 

maintenance of a steep bank across the channel from the bar. Channel deepening in these areas provides pool

Surveyed cross section on the Jacks Fork, Missouri, showing accretion of 

sediment in vegetation bands on a gravel bar. Sediment deposition occurs 

where hydraulic roughness is greater than surrounding areas due to 

dense growth of willows and sycamores. On the nearly vertical cut bank 

opposite the gravel bar, woody riparian vegetation provides minimal 

hydraulic resistance or erosional resistance.

MISSOURI

ARKANSAS

IL

OK

Map Area

Ozark Plateaus

Missouri Riv er

Jacks Fork

MISSOURI

ARKANSAS

I L

O K

Springfield

Ozark

Plateaus

0

0 100 MILES

100 KILOMETERS

Riparian Vegetation and Maintenance of Physical Habitats—

Missouri

26 
habitat in stream reaches that are otherwise uniform and shallow. In riffles, erosion around dense vegetation 

creates complex channels with diverse, closely spaced habitats.

The studies also determined that riparian vegetation was not effective in stabilizing banks in many Ozarks streams 

where bank height exceeds rooting depth. In these cases, the roots do not strengthen the bank near the stream 

surface. Because the lower part of the bank is not strengthened, it erodes easily during floods. The unstable, 

undercut banks that result from this process slump into the stream, supplying readily transportable sediment.

For more information refer to Jacobson and Pugh (1997), McKenney and others (1995), and Pflieger (1989). 

Growth of woody vegetation in bands 

increases hydraulic flow resistance on the 

gravel bar, resulting in deposition of ridges 

of gravel and sand within the vegetation 

bands. As gravel is deposited in the 

vegetation bands, the channel flow is 

constricted, resulting in a narrower 

channel and deeper, swifter flows along 

the opposite side of the channel.

Riparian vegetation provides hydraulic 

flow resistance and erosional resistance, 

both of which can contribute to channel 

stability. In gravel-bed streams of the 

Ozarks, willows and sycamores colonize 

unstable gravel bars in distinctive bands.

27
28 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

EXPLANATION

DEPTH, IN METERSDEPTH, IN METERS

Rocheport

MISSOURI

Missouri Riv er

0 430

0

2

4

6

8

10

12

0 387

0

2

4

6

8

10

12

DISTANCE ALONG TRANSECT, IN METERS. VERTICAL SCALE GREATLY EXAGGERATED.

DOWNSTREAM

WATER VELOCITY,

IN CENTIMETERS

PER SECOND

280

220

160

100

40

–20

–80

64

64 66 68 70

72 74 76

78

66

Bathymetry, accoustic doppler 

current profile

Bank

Revetment

Wingdam

NAVIGATION CENTER LINE

THALWEG

0.5 KILOMETERS

0.5 MILES0.25

0.250

0

Figure 15. Bathymetry and velocity data from a navigational reach of the Missouri River near 

Rocheport, Missouri. All transects are viewed looking downstream with the current velocity projected 

into the line of the transect. The velocity data obtained by an acoustic Doppler current profiler show 

complex flow fields around wing dams. Dark blue colors in the velocity profiles indicate negative 

velocities—that is, current velocity in the upstream direction. These areas occur in large eddies 

downstream of wing dams. The main thread of current is shown as hot colors, with velocities as much 

as 250 centimeters per second. Also, the bottom topography of the river shows a complex of deep and 

shallow areas related to the navigation structures. Although quite unlike the shallow, braided stream 

channel morphology that existed prior to emplacement of navigation structures, the structured 

channel still has substantial habitat diversity. (Continued on page 29.)
FACTORS AFFECTING PHYSICAL STREAM HABITAT 29

neering functions as well as providing cover, substrate, 

and hydraulic refugia (Gore and Shields, 1995).

Land-use changes that alter vegetation conditions in the 

riparian zone can substantially affect hydraulic resistance and erosion resistance with consequent effects on 

stream habitat. Removal of large woody debris from the 

channel (snagging), agriculture, forestry, and grazing 

practices that decrease hydraulic and erosion resistance 

are widespread on many landscapes. Lowered flow 

resistance increases velocity, thereby decreasing stage 

for a given discharge. Because of this effect on stage, 

vegetation and wood debris have been removed through 

the process of snagging in many areas as a flood-control 

DEPTH, IN METERS DEPTH, IN METERS

DEPTH, IN METERS DEPTH, IN METERS

0 400 0 412

0

2

4

6

8

10

12

0

2

4

6

8

10

12

0 538

0

2

4

6

8

10

12

0 418

0

2

4

6

8

10

12

0 430

0 430

0

2

4

6

8

10

12

0

2

4

6

8

10

12

DEPTH, IN METERSDEPTH, IN METERS

DISTANCE ALONG TRANSECT, IN METERS. VERTICAL SCALE GREATLY EXAGGERATED.

DISTANCE ALONG TRANSECT, IN METERS. VERTICAL SCALE GREATLY EXAGGERATED.

DISTANCE ALONG TRANSECT, IN METERS. VERTICAL SCALE GREATLY EXAGGERATED.

DOWNSTREAM

WATER VELOCITY,

IN CENTIMETERS

PER SECOND

280

220

160

100

40

–20

–80

78

70 76

74

72

68

Figure 15—Continued. Bathymetry and velocity data from a navigational reach of the Missouri 

River near Rocheport, Missouri. 
30 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

measure (Shields and Nunnally, 1984). Decreases in 

vegetation also commonly decrease erosion resistance 

of banks because of decreases in cohesive strength provided by roots. As a result, the rate of bank erosion and 

channel migration may increase, with resultant habitat 

disturbance and changes in sediment yield. Recently, 

Waters (1995) has argued that sediment yield from 

unstable, eroding riparian zones has been vastly underestimated as a source of nonpoint source pollution.

Livestock grazing in riparian zones has been implicated 

in many studies as a direct cause of habitat degradation 

(Platts, 1990; Meyers and Swanson, 1992; Trimble and 

Mendel, 1995). Livestock decrease vegetation densities, which in turn decrease hydraulic resistance and 

erosional resistance. In a controlled exclosure experiment of the effects of cattle on streambank erosion, 

Trimble (1994) determined that the effects of riparian 

vegetation were of secondary importance in controlling 

bank erosion compared to the direct trampling effect of 

cattle. Trimble identified cow ramps—areas where cattle consistently entered and exited the stream channel—as focal points for bank erosion and sediment 

yield in areas of high grazing density.

Although decreases in woody riparian vegetation commonly have been associated with channel instability 

and habitat degradation in humid parts of North America, regrowth of riparian vegetation does not necessarily 

have an immediate or beneficial effect on streams. In 

small streams in Wisconsin, Trimble (1997) determined 

that stream reaches with woody riparian vegetation 

were wider and shallower than comparison reaches with 

grassy vegetation. Trimble attributed this trend to the 

increased complexity of secondary currents around tree 

trunks and large woody debris that tended to widen the 

channel. The net effect on stream habitats in these Wisconsin streams is unknown, but the increased width-todepth ratio noted in wooded stream reaches could be an 

indicator of relative loss of pool habitats. In the Missouri Ozarks, Jacobson and Pugh (1997) showed that 

woody riparian vegetation had a negligible effect on 

bank erosion rates; they attributed this lack of stabilization in part to the oversteepening of banks that diminished the erosion resistance function of tree roots (fig. 

6).

Riparian vegetation not only contributes to hydraulic 

resistance and erosion resistance, but also provides 

organic material, shading, cover, and delivery of large 

woody debris. Organic material provides the basis of 

the food chain. Delivery of organic material is enhanced 

when woody vegetation borders the stream channel. 

Retention of organic material within a stream reach is 

determined by physical factors such as hydraulic complexity and connection of the channel with off-channel 

water bodies. Shading is largely a function of canopy 

closure over a stream. Riparian land-use changes that 

decrease shading can increase temperatures and temperature fluctuations and increase primary productivity. 

Hence, the net effect of decreased shading should be 

evaluated in the context of trophic levels, food, and 

energy dynamics within a basin (Hicks and others, 

1991).

Cover and habitat complexity are positively associated 

with large woody debris delivered to stream channels 

(fig. 16). Comprehensive literature is available on the 

benefits of large woody debris in providing physical 

habitat and the relations between riparian land use and 

large woody debris dynamics (for example, Swanson 

and others, 1976; Gippel, 1995; Keller and others, 

1995; Wood-Smith and Buffington, 1996). In general, 

large woody debris provides cover, hydraulic diversity, 

and pool habitats. Large woody debris also provides 

substrate for some types of invertebrates. The net effect 

of large woody debris on stream habitat is a function of 

the size of the channel (individual large woody debris 

pieces have less effect on channel morphology in larger 

channels than in smaller ones), the rate at which large 

woody debris is delivered to streams (usually through 

bank erosion), the rate at which it moves through stream 

reaches, the rate at which it rots or otherwise breaks 

down, and the potential for large woody debris to be 

buried by sediment. The role of large woody debris also 

increases in complexity as individual pieces interact to 

form multi-piece obstructions to flow (Abbe and Montgomery, 1996).
INVESTIGATING THE LINKS BETWEEN LAND-USE AND PHYSICAL STREAM-HABITAT CHANGES 31

INVESTIGATING THE LINKS BETWEEN LAND-USE 

AND PHYSICAL STREAM-HABITAT CHANGES

Some of the links between land-use changes and stream 

habitat changes are direct and clearly defined, whereas 

others are difficult or impossible to establish with confidence. Generally, cause and effect are more easily 

linked the closer they are to each other in time and 

space. For example, causal links can be identified with 

considerable confidence when considering channel 

degradation and loss of spawning habitat directly downstream from a dam. The strength of the link and ability 

to quantify the effect diminishes as downstream tributaries add water and sediment, as energy is expended, 

and as opportunities increase for sediment in transport 

to be deposited on bars and flood plains. Similarly, the 

cause of stream siltation directly downstream from an 

instream aggregate mine may be inferred with confidence, but the cumulative downstream effects of timber 

management that has varied spatially and temporally in 

a drainage basin over several decades may be quite difficult to separate from other natural- and anthropogenic-induced sources of disturbance.

Studies designed to establish links and evaluate the sensitivity of physical stream habitat to land-use changes 

vary considerably in their design and ability to discern 

links. Studies have been classified into four main 

approaches: historical, associative, process, and modeling. Some investigations use more than one approach to 

develop greater understanding over suitable scales of 

space and time. Historical approaches evaluate the 

sequence of land-use changes and effects over long time 

periods and take advantage of existing data. A historical 

approach often is needed to evaluate a reference state 

for a stream habitat and whether or not a stream is in the 

process of adjusting to previous disturbances. An associative study could be used to explore multivariate correlations of habitat conditions with different land uses. 

This approach can establish effects of spatially varying 

factors and can, in some cases, be used to identify factors that control habitat sensitivity to land-use change. 

Process-based approaches can be used to provide complimentary information that quantifies short-term links 

and responses in a more controlled setting where processes can be measured in an experimental or monitoring framework. A modeling approach can be used to 

provide a predictive understanding for extrapolating 

results to other sites and conditions.

Historical Approaches

Historical data provide an important long-term framework for evaluation of land-use and habitat links. Historical data can define a reference condition for 

assessment of the magnitude of habitat change, can be 

used to assess variability and trends for a specific time 

period, and can be used to correlate historical land-use 

changes with documented ecosystem responses. Historical approaches to understanding the links between 

land-use changes and stream habitat are especially 

important when dealing with land-use changes at the 

Figure 16. Accumulation of large woody debris on 

Little Piney Creek, Missouri. Large woody debris 

accumulations were removed or burned by early 

settlers to decrease flood hazards and improve 

conditions for floating railroad ties down the river. In 

the past 50 years, increased riparian woodland area 

has caused more large woody debris to enter the 

stream channel, and in some places along the 

channel, large woody debris concentrations are 

sufficiently high that log jams are beginning to 

reform. Although studies have shown that woody 

riparian vegetation does not act to stabilize channel 

migration on this river (Jacobson and Pugh, 1997), 

bank erosion and consequent delivery of large 

woody debris to the channel provides essential 

stream habitat. The location of Little Piney Creek is 

shown in the section “Establishing Land-Use History 

and Habitat Links—Missouri” on p. 32.
32

Many common land uses disturb the landscape at low 

to moderate intensities over broad areas and long time 

intervals. Agriculture and forestry are two prominent 

examples. Their effects on streams are persistent and 

cumulative rather than acute and direct. In addition, many 

landscapes have multiple land uses and natural disturbances 

that could affect physical stream habitat. In these situations, 

the links between land-use changes and stream habitat 

changes can be difficult to establish.

In cooperation with the Missouri Department of Conservation and the National

Park Service, the USGS has been evaluating links between land-use history and 

habitat changes in streams in the Ozarks of Missouri. Timber-cutting practices in 

the late 1800’s to early 1900’s were thought to be responsible for extensive stream 

instability and gravel aggradation in the Ozarks. However, a systematic evaluation of the 

potential for land-use changes to disturb streams produced different conclusions. Among many interacting landuse and climatic disturbances, livestock grazing in riparian areas probably was the most direct and damaging 

land-use link to stream instability.

To understand the key links between land-use changes and stream changes requires the development of historical 

information. In the Missouri Ozarks, the USGS documented land-use changes using a considerable range of data 

sources, including primary historical documents such as land deeds and explorers’ diaries, Government Land 

Office records, U.S. Census data, old landscape photographs, oral histories, archival aerial photography, maps, 

and satellite imagery. Among these sources, oral historical information proved especially helpful in establishing 

specific agricultural and timber-cutting practices and how these practices might have disturbed streams.

Historical data from old photographs, 

census records, and oral history can 

provide essential insight into land-use 

changes and the effects on stream 

habitats. Photograph courtesy of D. Ulmer.

Tie drives during the early 1900's in the 

Ozarks often carried 500,000 board feet of 

loose logs spread over 25 kilometers of 

river—usually during high flows (Jacobson 

and Primm, 1997). Photograph courtesy of 

the Ozark National Scenic Riverways 

collection; photographer unknown.

Map

Area

MISSOURI

Jack s Fork

Little

Current River

Piney

Van

Buren

Rolla

MISSOURI

0

0 50 MILES

50 KILOMETERS

Establishing Land-Use History and Habitat Links—Missouri
Historical records of stream responses were compiled from stratigraphic studies of flood-plain sediments, USGS 

stream-gage data (which can indicate large changes in streambed elevation), and historical aerial photography. 

The stratigraphic data were considered essential for evaluating a reference state for Ozarks rivers—what did 

streams look like and what was habitat availability under natural conditions before postsettlement land-use 

changes? These data indicated that streams had accumulated substantial quantities of gravel in the 

postsettlement period at the expense of fine (silt and clay) sediment. From these observations it was inferred that 

presettlement streams generally were narrower and deeper. In many parts of North America, intensive row-crop 

agriculture or grazing has resulted in accelerated upland soil erosion and aggradation of fine sediment in 

channels and flood plains. In contrast, Ozarks streams responded to postsettlement land-use changes by eroding 

fine sediment from flood plains and depositing substantial quantities of gravel. Streambed-elevation changes 

from the 1920’s to the 1990’s showed that postsettlement aggradation had ended in small basins, but waves of 

gravel continued to move downstream to accumulate in midsized basins. Hence, the land-use practices over the 

last century continue to cause channel instability and accelerated aquatic-ecosystem disturbance.

In the Ozarks, improved understanding of the historical links between land-use changes and stream-habitat 

changes has been useful in land, water, and fisheries management decisions. This understanding has allowed 

resource managers to focus concerns on riparian land-use changes that have had the most effect on streams. In 

addition, an understanding of the historical trends in disturbance has helped prioritize stream-habitat restoration 

efforts. With this understanding, restoration can be applied to streams that are at a stage of recovery rather than 

streams that are continuing to respond to historical disturbances.

For further information refer to Jacobson (1995), Jacobson and Primm (1997), Jacobson and Gran (1999), and 

Jacobson and Pugh (1992).

Historical data on channel changes. 

A, Stratigraphic data can be interpreted to 

illustrate how the channel morphology, 

energy, and sediment load has changed 

over time. Stratigraphic cross-sections can 

be compiled using bore-hole transects, 

trenching, or shallow geophysical methods. 

B, Streambed elevation data from U.S. 

Geological Survey stream-gage sites 

indicate long-term vertical changes in the 

streambed.

ELEVATION, IN METERS

ABOVE SEA LEVEL 

Silt loam

Sand

Gravel

Bedrock

240

230

220

Bore-hole

location

EXPLANATION

Postsettlement

Little Piney Creek

Presettlement

0 200 400

METERS, VERTICAL EXAGGERATION X 7

A.

0

2,000

500

1,000

1,500

1920 2000 1940 1960 1980

132

137

133

134

135

136

Current River at Van Buren, Missouri

DAILY MEAN

DISCHARGE, INCUBIC METERS

PER SECOND

MEAN STREAMBED

ELEVATION,5-POINT

MOVING AVERAGE, IN

METERS ABOVE SEA LEVEL

B.

33
34 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

scale of drainage basins (for example, Wissmar and others, 1994). Within drainage basins, the effects of landuse changes may not affect a stream reach for many 

years because sediment or channel adjustments are 

transmitted slowly within the channel network. As 

basin size increases, the opportunities for more sources 

of variability increase. In turn, increases in variability 

increase the need to separate background variation from 

climatic events and natural complex responses of the 

drainage basin from the effects of land use (Ryan and 

Grant, 1991).

Historical data can help in defining a reference state, a 

prerequisite to environmental assessment. A reference 

state may define an acceptable condition—for example, 

a percent channel area occupied by pool habitat at a particular discharge. Definition of acceptable reference 

states frequently requires application of some judgment 

of optimal ecosystem functioning. Because this optimality often implies subjective judgment of the worth 

of some species or functions over others, the reference 

state commonly is defined instead as the natural condition of the river or reach and to assume that the natural 

condition optimized ecosystem characteristics such as 

diversity and abundance.

Historical analysis of a river system can provide a 

description (ranging from qualitative to quantitative) of 

the natural condition of a river for a period preceding 

land-use disturbance (fig. 17). Historical analysis also 

can contribute to defining variability of a river system 

before, during, and after some historical disturbance. 

This type of understanding is necessary for many restoration and mitigation efforts in which it is desirable to 

know if a river system presently is in a degraded or 

unstable state. Where historical data are exceptionally 

good, correlations with historical disturbance events 

can provide a complete history of disturbance, reaction, 

and recovery of the river system. Past responses of 

physical habitat to known disturbances probably are the 

best indicators of future responses.

Historical data can come from many sources (Jacobson 

and Primm, 1997; Kondolf and Larson, 1995). These 

sources vary widely in scale, resolution, and reliability. 

Some historical data were collected originally for purposes completely unrelated to an evaluation of links 

between land-use changes and habitat responses; as the 

only data available for historical time frames, these data 

are extremely valuable, but often they require careful 

interpretation and professional judgment.

Observations of sediment characteristics, stratigraphic 

relations, and soil formation characteristics of floodplain sediments allow interpretation of how rivers have 

responded to historical and prehistorical changes in 

hydrology and sediment yield (for example, Trimble, 

1974; Knox, 1977; Magilligan, 1985; Jacobson and 

Coleman, 1986). Even with extremely detailed stratigraphic data and reliable dating of deposits, stratigraphic analysis may provide only a qualitative or semiquantitative description of a river-system changes. In 

cases where land-use changes have been substantial, 

this level of analysis can provide useful information. 

For example, Jacobson and Coleman (1986) documented aggradation of flood plains in the Maryland 

Piedmont and attributed the aggradation to increases in 

sediment load coincident with farming practices during 

1730–1930. However, within the accuracy of stratigraphic methods and without direct historical data, 

these authors could only infer the relative contributions 

of hydrologic and sediment-yield changes. In cases 

where the effect of land use has been small compared to 

climatic background variation, stratigraphic analysis 

may not resolve the effects of land-use change.

As the time interval of interest nears the present, the 

number, detail, and reliability of historical data sources 

generally increase. U.S. Census records, aerial photography, satellite imagery, climatic records, and economic 

records can document potential land-use stressors. 

Hydrologic records, aerial photography, surveys of 

river sections at bridge crossings, historical maps, sediment and water-quality data, and reservoir resurveys 

can supply the information needed to document and 

evaluate effects on physical habitat (for example, Wolman, 1967; Costa, 1975; James, 1991).

In some cases the spatial and temporal relations 

between land-use and habitat effects will be clearly 

defined. For example, channel straightening may cause 

nearly immediate channel incision that would cause an 

abrupt change in the stage-discharge relation (“rating 

shift”) of a nearby stream gage (for example, Simon and 

Robbins, 1987). In this case, the causal link between 

stream straightening and channel incision is quite clear. 

In many other cases, the data may be sufficient only to 

constrain possible interpretations. For example, McIn-
INVESTIGATING THE LINKS BETWEEN LAND-USE AND PHYSICAL STREAM-HABITAT CHANGES 35

0

0 5 10 MILES

5 10 KILOMETERS 

EXPLANATION

1879 Channel

1991 Channel

Data from Scientific Assessment and Strategy Team Digital Data Archive,

Eros Data Center, Sioux Falls, South Dakota. Albers Equal Area Projection 

93°07'30" 93° 92°52'30"

38°15'

38°07'30"

Valley wall

Valley wall

Glasgow

Figure 17. Channel positions of the Missouri River near Glasgow, Missouri, 1879 and 

1991. Historical analysis of channel changes is important for evaluating the 

magnitude of land-use effects and determining reference conditions for restoration 

activities. In the case of the Missouri River, flow regulation and navigation structures 

have changed the river from a braided system with transient sand islands and 

multiple shifting, shallow channels to a meandering stream with stable banks, greater 

average depths, higher average velocities, and many fewer connections between the 

channel and flood-plain habitats.

tosh and others (1994) were able to document changes 

in fish habitat in eastern Oregon and Washington by 

comparing survey data from 1934 to 1942 with resurveys between 1990 to 1992. These historical snapshots 

provided a strong assessment of change, but the causal 

links to land-use history had to be inferred because 

detailed measurements of conditions were not available 

for the broad study area for the time interval studied.
36 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

Associative Approaches to Land Use—Habitat Links

Links between land use and stream habitat can be 

assessed through studies that associate or correlate 

basin-scale or riparian land use with measured habitat 

variables. Broad-scale associations are of interest for 

developing general understanding of regional controls 

on habitat availability and for developing regional 

water-quality evaluations. Associative studies can be 

used as coarse filters of potential links between land use 

and stream habitats before efforts are spent on other, 

more time-intensive approaches.

Extensive associative studies and assessments typically 

make use of integrated indices to evaluate health of rivers and streams. Most of these indices incorporate some 

measure of habitat quality along with biological characteristics. The U.S. Environmental Protection Agency’s 

(USEPA) Rapid Bioassessment Protocol (RBP) is an 

example of a method used to conduct cost-effective biological assessments of streams and rivers. The RBP 

method attempts to provide an integrated assessment of 

habitat and stream community measures in comparison 

to a defined reference situation. The RBP method has 

been used to characterize the existence and severity of 

stream impairment through associations with land-use 

practices, to identify sources and causes of impairment, 

to evaluate the effectiveness of control actions, or to 

characterize regional biotic characteristics. Other indices also are used to characterize habitat in associative 

studies. The Ohio Environmental Protection Agency’s 

Qualitative Habitat Evaluation Index (QHEI), for example, is widely used in midwestern assessments (Rankin, 

1995).

Associations for Assessing Habitat Availability

Associative studies can determine broad relations 

between land use and habitat availability. These types 

of studies often are useful for regional management of 

biological resources and sport fisheries. The value of 

associative studies for resource management depends 

on identifying reliable correlations between measured 

land-use characteristics and habitat availability. 

Because of the complex geomorphic and hydrologic 

response of drainage basins to land-use changes and the 

confounding effects of interacting land-use changes and 

natural disturbances, such studies frequently encounter 

difficulties in determining cause and effect. Nevertheless, associative studies can serve as useful indicators of 

landscape-scale effects of land use on stream habitats 

(Richards and others, 1996).

Many studies have attempted to document associations 

between land use and instream habitat availability and 

use. Based on these studies, channel substrate seems to 

relate most readily to land-use changes. Substrate characteristics are considered one of the most important factors in distributions of macroinvertebrates and some 

fish guilds (Berkman and Rabeni, 1987). For example, 

channel substrate embeddedness and invertebrate community composition have been shown to vary systematically with basin-scale variables such as amount of 

urbanization and agricultural land use (Richards and 

Host, 1994). 

Links between basin-scale land use and channel geometry have been harder to document except in cases of 

extreme land-use change such as urbanization 

(Leopold, 1994). Even in cases of urbanization, complex responses of channels to the balance of hydrologic 

and sediment response can cause unexpected results 

(Odemerho, 1992). The difficulty in relating basin-scale 

land use to channel geometry results from the many 

geologic, riparian, and hydrologic factors that can additionally affect channel geometry. For example, Ryan 

and Grant (1991) documented that suspected associations between timber-harvesting activity in southwest 

Oregon and active channel width were obscured by several factors including the spatial complexity of slopechannel interactions and large historical floods. Similarly, in central Michigan, channel width was associated 

more with bedrock geology and structure than with land 

use (Richards and others, 1996). A better statistical relation was obtained discriminating channel conditions 

between drainage basins with and without timber harvesting in southern Alaska (Wood-Smith and Buffington, 1996). The strength of this relation apparently was 

because of the direct links between timber harvest practices and pools that were associated with large woody 

debris.

The numerous studies that document association do not 

necessarily identify causality that could lead to a better 

understanding of the link between land use and habitat. 

Because of the complex, lagged responses that are possible in landscapes, instream habitats may be affected 

by land uses that existed at some time in the past, or 
INVESTIGATING THE LINKS BETWEEN LAND-USE AND PHYSICAL STREAM-HABITAT CHANGES 37

habitat conditions at one point in time may be relict 

from a single large flood or drought in the past. Moreover, it can be difficult to establish which of many landuse practices in a drainage basin is responsible for 

observed habitat characteristics. For example, channel 

substrate and cross-sectional morphology may be 

affected by basin-scale effects on runoff and sediment 

yield (Richards and others, 1996) by local land-use in 

the riparian zone (Rabeni and Smale, 1995), or by both. 

Associative studies may not be able to measure processes with sufficient resolution to determine the source 

of channel disturbance, but such studies provide valuable data constraining possible sources.

Associations for Water-Quality and Environmental 

Assessments

Broad-scale water-quality and environmental assessment programs typically seek to evaluate associations 

between land use and habitat to provide comparable 

assessments using bioindicators. In such programs, 

stream biota are the primary interest because they are 

robust and integrative indicators of water quality and 

overall biological integrity (Plafkin and others, 1989). 

However, stream biota also are affected by physical 

habitat, so the physical differences must be considered 

in comparing sites:

“Habitat, as affected by instream and surrounding topographic features, is a major determinant of aquatic community potential. Both the quality and quantity of 

available habitat affect the structure and composition of 

resident biological communities. Effects of such features can be minimized by sampling similar habitats at 

all stations being compared. However, when all stations 

are not physically comparable, habitat characterization 

is particularly important for proper interpretation of biosurvey results.” (Plafkin and others, 1989, p. 2–4)

The need for physical habitat characterization in waterquality studies also is stated by Rankin (1995, p. 181):

“A key concept of the Clean Water Act is the protection 

of biological integrity of the streams and rivers of the 

United States. Basic to maintaining diverse, functional 

aquatic communities in surface waters is the preservation of the natural physical habitat of these ecosystems.”

Several national programs seek to address associations 

between land use and the aquatic community as part of 

water-quality or environmental assessment.

The USGS National Water Quality Assessment 

(NAWQA) Program, which started in 1991, is intended 

to provide a nationally consistent description of the 

water-quality conditions for a large part of the Nation’s 

water resources. The NAWQA Program has structured 

its sampling efforts toward establishing multiple lines 

of evidence of stream health, water-column chemistry, 

bed sediment and tissue contaminant surveys, and ecological surveys (fish, invertebrates, algae, and multiplescale physical habitat). These investigations are being 

conducted on a rotational basis in more than 50 study 

units throughout the Nation, which incorporate about 

60 to 70 percent of the water used and population 

served by public water supplies. Biological, habitat, and 

water-quality data are compared to basin-wide and local 

land use to identify associations between land use and 

stream health. The NAWQA Program sample sites have 

been selected specifically to compare contrasting landuse effects on water quality, and physical habitat assessment is used for necessary baseline information on 

environmental settings. Associations noted in the 

NAWQA Program study units (for example, Goldstein 

and others, 1996; Maret and others, 1997) provide useful inter-site comparisons of habitat effects on biota and 

generate hypotheses for more detailed investigations of 

links between land use and stream communities.

The USGS also is conducting a national-scale study, the 

Biomonitoring of Environmental Status and Trends 

(BEST) Program, designed to identify and understand 

the effects of environmental contaminants on biological 

resources, particularly those resources located on U.S. 

Department of the Interior lands, at the national, 

regional, and local levels. The BEST Program is 

focused on the use of bioassessment for evaluation of 

contaminants in the environment and includes terrestrial as well as aquatic species. The role of contaminants 

is evaluated by comparison with the roles of habitat limitations and biotic interactions in determining species 

health. A summary of the BEST program is found in 

Schmitt and Dethloff (2000).

The USEPA’s Environmental Monitoring and Assessment Program (EMAP) is a long-term program 

intended to document and assess the condition of the 

Nation’s environmental quality change (U.S. Environmental Protection Agency, 1990). The EMAP focuses 

mainly on national and regional scales for extended 

periods of time—years to decades. The EMAP collects 
The U.S. Geological Survey 

(USGS) began implementation 

of the National Water-Quality 

Assessment (NAWQA) Program 

in 1991 to provide a nationally consistent description of 

current water-quality conditions, 

define long-term trends, and 

to identify, describe, and explain 

the major factors that affect 

water quality for a large part of 

the Nation's surface- and groundwater resources. When fully 

implemented, the NAWQA program 

will include 51 study units, which 

incorporate parts of most major 

river basins and aquifer systems 

in the United States. This nationwide database will provide abundant 

information for associative-level studies to correlate stream habitat, 

stream biota, and water quality with drainage-basin level descriptors of land use.

The 51 study units will be rotated through a cycle of intensive field data collection and a low intensity phase. The 

first 20 study units began in 1991 and continued through 1996. The second 16 study units began in 1994, and the 

third set of 15 study units began their investigations in 1997. Intensive water-quality and biological investigations 

are conducted for 3 years, followed by 5 to 6 years of low-level monitoring, with the cycle perpetually repeated. 

The first set of 20 study units will restart their intensive phase in 2001. Many cooperative projects have been 

generated from these NAWQA studies due to the information gained. 

The initial phase of the Ozark Plateaus NAWQA study unit began 

in 1991. The study unit is approximately 122,900 square 

kilometers (48,000 square miles), and includes parts of 

Missouri, Arkansas, Oklahoma, and Kansas and is drained 

by seven major river basins. Land use is primarily forest and 

agriculture (includes pasture and cropland). 

Longitudinal and transverse surveys and 

permanent vegetation plots were established at 

13 sites in the Ozark Plateaus study unit. Resurveys 

of these sites will give information on the movement of the stream channel and changes in the 

riparian vegetation over time.

1991–95

1994–98

1997–2001

Not yet scheduled

High Plains Regional

Ground Water Study, 

1999-2004

NAWQA Study Units— 

Assessment schedule

MISSOURI

OKLAMHOMA ARKANSAS

KANSAS NAWQA Program

Ozark Plateaus

Study Unit

Land-Use Characteristics and Aquatic Community Structure—

Ozark Plateaus NAWQA Study Unit

38
The 1990 population within the study unit was approximately 2.3 million people. Data analyses from 41 sites in 

the Ozark Plateaus study have shown multiple lines of evidence of elevated concentrations of trace elements in 

the water column, bed sediments, and tissue samples collected in basins with mining land use. Data collected 

from sites with predominately agricultural land use have shown elevated concentrations of nutrients, bacteria, 

and agrichemicals in the surface and ground water and have characteristic fish community structures (Davis and 

Bell, 1998; Petersen, 1998).

Associations between land use and physical habitat have been more subtle than those between land use and 

chemical habitat. Sites in basins with predominantly agricultural land use tended to have more open canopies, 

steeper segment gradients, and more sinuous stream channels than the forested sites. Sites in predominantly 

forested basins tended to have deeper and swifter flow, smaller channel widths, and more dense woody riparian 

vegetation (at small basin size) than the agricultural sites (Femmer, 1997). Of the land use-habitat associations 

studied, canopy opening, channel width, and channel sinuosity were thought to result, at least in part, from 

agricultural practices. Associations between land use and water velocity, sideslope gradients, and flood-plain 

widths were not thought to reflect cause/effect linkages (Petersen and others, 1998). Also, the most dramatic 

association between land use and fish communities in this dataset was an increase in relative abundance of 

stoneroller minnows at agricultural sites. The greater relative abundance was thought to result in part from 

chemical habitat—increased nutrients—and, in part, from physical habitat—open canopies and wider channels 

that encourage algae growth (Petersen and others, 1998).

Ecological surveys of fish, invertebrate, and algal 

communities were conducted at a subset of 41 sites 

in the Ozark Plateau s study unit. Ecological surveys 

were conducted for 3 consecutive years and at three 

sites at multiple reaches to reduce year-to-year

and reach-to-reach variation. 

Information such as bank height, bank angle, channel 

width, canopy angles, and stream-bed substrate was 

collected at each site. This reach scale data is combined 

with segment and basin scale data to characterize the 

basin upstream of the site.

39
40 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

data on the ecological condition of randomly selected 

sites from multiple ecosystems with the intent of integrating these data to assess environmental change (U.S. 

Environmental Protection Agency, 1990). Within the 

EMAP framework, land use is considered a stressor 

indicator and habitat conditions are considered exposure indicators; ultimately, correlations among indicators within the EMAP data base will be investigated 

(U.S. Environmental Protection Agency, 1990).

Process Studies of Land Use—Habitat Links

Cause-and-effect links between land-use changes and 

stream habitat can be more firmly established by focusing on detailed process measurements or developing 

well-controlled field experiments (fig. 18). Because of 

cost constraints, such approaches usually are more limited in scope than historical or associative approaches. 

Process studies typically focus on either drainage-basin 

scale measures (changes in runoff, peak flows, or sediment yield) or channel-scale measures (changes in habitat volume, substrate characteristics, or channel 

morphology). In some cases, multiscale and multidisciplinary studies have been designed to synthesize 

detailed process measurements at the drainage-basin 

and channel scales. Examples of these include studies 

associated with the Long Term Ecological Research 

Sites, sponsored by various universities, USDA-USFS, 

and the National Science Foundation, at the H.J. 

Andrews Experimental Forest, Blue River, Oregon, and 

the Coweeta Hydrologic Laboratory, Otto, North Carolina, and interagency multidisciplinary work centered 

on Redwood Creek Basin, northern California (Nolan 

and others, 1995).

Study designs for process-level approaches generally 

involve comparisons of habitat responses between treatment and control sites or monitoring of a single site 

before, during, and after a land-use disturbance. Paired 

drainage-basin experiments have long been used to 

evaluate hydrologic and sediment-yield changes due to 

agricultural or forestry practices (for example, Hornbeck, 1975). More powerful, however, are paired basin 

designs that also measure processes before, during, and 

after land-use change (for example, Jones and Grant, 

1996).

At the channel scale, experiments may involve intentional changes to the channel or may rely on monitoring 

a natural sequence of events. Manipulative experiments 

create conditions with considerable control for testing 

specific hypotheses. For example, Smith and others 

(1993) removed all large woody debris from a small, 

gravel bed stream in Alaska and evaluated the effects on 

channel morphology over 4 years using a high density 

of periodically resurveyed channel cross sections. The 

detailed control over the disturbance (large woody 

debris removal) and high resolution measurement of the 

response allowed the investigators to evaluate quantitatively the link between large woody debris and channel 

morphology and habitats.

Figure 18. Detailed measurements are

made to study land-use effects on stream

geomorphology and habitat in the Ozark

region of Arkansas. Unlike manipulative

field experiments in which experimental

treatments are imposed by scientists with

considerable control, monitoring

experiments rely on an opportunistic time

series of changes to provide insights into

processes and rates of processes of

habitat changes. Such monitoring studies

may record the effects of land-use or

climatic disturbances, but even if

substantial changes do not occur during

the monitoring period, these studies

provide important documentation of

background rates of change.
INVESTIGATING THE LINKS BETWEEN LAND-USE AND PHYSICAL STREAM-HABITAT CHANGES 41

An example of a controlled field experiment was the 

spring 1995 controlled flood on the Colorado River in 

the Grand Canyon. This experiment utilized a design 

discharge from Glen Canyon Dam to determine how the 

channel and associated habitats responded to a flow 

substantially larger than was normal under dam regulation. The main hypothesis tested was whether the 

design flood would be capable of redistributing sand to 

replenish sand bar and backwater habitats that had been 

lost due to flow regulation (fig. 19). Under tightly controlled experimental conditions, a multidisciplinary 

team was able to collect detailed and systematic data on 

the processes of habitat change (Collier and others, 

1997).

Direct manipulations of the stream systems are not 

always possible or cost effective. In many cases, 

detailed process measurements can be made in a monitoring environment in which experiments are run 

opportunistically as land-use change or other disturbances take place. For example, McKenney and Jacobson (1996) describe monitoring habitat change in 

Ozarks streams during a period of recovery from past 

land-use practices. During the monitoring period, the 

investigators also were able to document disturbance 

and recovery of stream habitats from a 50-year flood.

A. Preflood 

B. During the flood 

C. Postflood

ARIZONA

Glen Canyon Dam

Colorado River

Figure 19. Experimental flood on the Grand 

Canyon. This controlled field experiment 

was designed to evaluate the effects of 

flood flows on habitat and biological 

resources of the Colorado River in the 

Grand Canyon (Collier and others, 1997). A 

specific hypothesis was tested that the 

design flow would be sufficient to suspend 

sand that had accumulated in the channel 

bottom (A and B) and redeposit it on 

channel margins where it would 

regenerate backwater and sand bar habitat 

(C). (Figure from Anderson and others, 

1996.)
0.5 MILES

0

0

0.5 KILOMETERS

. .

.

Basin boundary

Pasture

Equals 50

dairy cows

EXPLANATION

Water-quality site

Farm

 sampling site

Invertebrate -

Town

Lampeter

TREATMENT

BASIN

76°15'30"

CONTROL BASIN

Willow Street

76°15'58"

39°59'40"

T-1

C-1

T-4

T-2

T-3

39°59'52"

•

• •

•

Manipulative experiments are designed to explore how 

alluvial systems behave under relatively well-controlled 

conditions. By controlling specific variables, some of the 

inherent variability of the natural system can be accounted 

for. Such an experiment is underway in a subbasin of Mill 

Creek in southeast Pennsylvania to attempt to isolate the effect 

of livestock grazing on stream health. The study is being conducted by the 

USGS in cooperation with the Pennsylvania Department of Environmental 

Protection. The primary objective of this study is to evaluate the effect of 

exclusion of livestock from stream reaches on surface- and ground-water quality. 

The use of benthic macroinvertebrate community data to assess stream health requires 

evaluation of physical habitat changes accompanying exclusion.

The study uses a paired basin design with additional pre- and postexclusion and upstream and downstream 

analyses. Two adjacent subbasins of Mill Creek with similar agricultural land use, climate, topography, geology, 

and size (about 5 square kilometers) were selected. Both subbasins have substantial numbers of dairy cattle that 

had unlimited access to the stream channel in the pre-exclusion period. After a period of pre-exclusion data 

collection, streambanks in four treatment reaches were fenced. The prefencing period was 1993 to 1997, and the 

study will continue to November 2001.

A comprehensive suite of chemical, physical, and biological data are being collected in treatment and control 

sites. The data collection is designed to detect significant variations in measured constituents under base-flow 

and runoff conditions. Biological indices are being used to indicate the overall health of the streams using the 

assumption that the biological community structure is sensitive to physical and chemical habitat. Benthic 

macroinvertebrates were chosen as an index of stream health and as an appropriate metric for comparing to 

designated uses of the stream. Absence of pollution sensitive taxa such as Ephermeroptera (Mayflies), Plecoptera 

The Mill Creek Basin, Southeastern Pennsylvania. Treatment stream segments have cattle 

excluded from them by fencing, whereas control stream segments have open access of 

dairy cattle to the stream.

Mill Creek Cattle Enclosure Study—Pennsylvania

42

Lancaster

Study

basin

PENNSYLVANIA

S usquehanna

R

M

Map Area ill Ck

PENNSYLVANIA

0 25 KILOMETERS

0 25 MILES
(Stoneflies), and Trichoptera (Caddisflies) generally is considered to be indicative of poor water quality, if other 

abiotic and biotic factors are not limiting. Dominance by a single taxa, low taxa richness, or differences in 

community structure compared with reference sites also are considered to be useful indicators of stream health 

(Plafkin and others, 1989). The Mill Creek study design incorporates community, population, and functional scores 

into a biological evaluation. Channel width, depth, and velocity are surveyed at each site during invertebrate 

sampling to record physical changes in stream channel habitats and to account for habitat effects on the biotic 

communities.

For further information refer to Galeone and Koerkle (1996), Galeone (1999), and Plafkin and others (1989). 

Kick-net sampling of stream benthic invertebrates 

in the Mill Creek Basin, Pennsylvania, cattle enclosure 

experiment. Changes in benthic invertebrates will be 

compared between streams with and without cattle 

access, and before and after cattle are excluded. 

The direct control of disturbance and detailed 

measurements of physical, chemical, and biological 

responses will provide information on processes 

linking livestock grazing and stream biota. 

Photograph courtesy of D.G. Galeone, U.S. Geological 

Survey.

43
Rapid bank erosion is occurring in several 

areas on the Kenai River, Alaska. Boat 

wakes from private and guided fishing 

boats have been associated with rapid 

bank erosion. Increased sediment from 

bank erosion can adversely affect juvenile 

chinook salmon habitat, which is already 

in short supply. Photograph courtesy of 

J.M. Dorava, U.S. Geological Survey.

This controlled U.S. Geological Survey 

experiment determined that in sections of 

the Kenai River that allow motorboats, 19 

percent to 97 percent of the energy 

directed at the banks during the study 

period resulted from boat wakes. 

Photograph courtesy of J.M. Dorava, 

U.S. Geological Survey.

Rapid bank erosion on the Kenai River, 

Alaska, is caused by boat wakes from 

private and guided fishing boats. 

Increased sediment from bank erosion 

can adversely affect juvenile chinook 

salmon habitat, which is already in 

short supply. Because the recreational 

salmon fishery on the Kenai River 

contributes as much as $40 million 

per year to the local economy, bank 

erosion is a subject of regional concern. 

The USGS, in cooperation with the 

Alaska Department of Fish and Game, developed a 

streambank erosion monitoring program and performed a controlled 

boat-wake experiment to determine the effect of boat wakes on bank erosion.

Bank erosion was measured using erosion pins and sedimentation pans, and boat wake size was 

measured using specially designed boat wake gages. Erosion pins were installed in stream banks in two areas: 

areas that allowed the use of motorboats, and areas that were restricted to unmotorized boat use. This 

Anchorage

Kenai

Seward

Kenai River

SCALE 1:10,000,000

0 100 200 MILES

0 100 200 KILOMETERS

ALASKA

Map Area

ALASKA

Effect of Boat Wakes on Bank Erosion and Salmon Habitat—

Alaska

44
experimental design allowed the scientists to determine whether the erosion was caused by natural river 

processes or boat wakes. Erosion pins also were installed after the 1995 fishing season, measured before the 1996 

fishing season started, and measured after the 1996 fishing season ended, so that the timing of erosion could be 

compared to times of intense recreational use. Erosion pins also were installed in areas with bank-erosion control 

structures to evaluate the efficacy of mitigation measures such as coconut fiber logs, willow sprouts, spruce-tree 

revetments, rock riprap, and log revetments. Wake gages measure boat wake height and frequency, which can 

then be used to calculate the amount of energy directed at the bank by boat wakes. Erosion measurements 

collected during the off season and in areas where motorboats were restricted provide natural erosion rates for 

comparison. Streamgage data were used to calculate the erosive energy directed at the bank by the river currents 

without contributions by boat wakes.

As an additional analysis of the effects of boat wakes, controlled boat-pass experiments were performed with 

three different hull designs and variations in distance from the bank and passenger loading; each boat was driven 

at its maximum speed. During this experiment, wake heights were measured and sediment eroded from the 

banks was collected and measured in sedimentation pans attached to the banks.

This study determined that in sections of the Kenai River that allow motorboats, 19 to 97 percent of the energy 

directed at the banks during the study period resulted from boat wakes. Variations in boat wake energy are caused 

by different use levels, variations in fishing patterns, stream morphologies that concentrate or disperse natural 

and boat wake energy, and different boat travel patterns. The greatest bank erosion occurred when high 

streamflow coincided with high recreational boat use. Erosion in areas where the use of motorized boats is 

restricted was approximately 25 percent of erosion in the most popular, unrestricted boating areas. Among the 

bank-protection measures investigated, all were equally effective at reducing boat wake heights and slowing 

erosion. A spruce-tree revetment provided the most habitat for juvenile salmon.

For more information refer to Dorava and Liepitz (1996), Dorava and Moore (1997), and Dorava (1999).

Experimental boat passes used boats with three 

different hull designs, varied distances from the 

bank, and different passenger loads to determine 

effects of the different combinations on boat wake 

size and bank erosion. Photograph courtesy of J.M. 

Dorava, U.S. Geological Survey.

45
46 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

Modeling Links between Land Use and 

Physical Stream Habitat

Links between land-use changes and habitat responses 

can be portrayed with physically based models. Currently (2000), models exist at two spatial scales, with 

little overlap. Basin-scale models are designed to predict or analyze how changes in land use affect basin 

hydrology and sediment yield. Channel-scale models 

are designed to predict or analyze how channel morphology and habitat availability vary with discharge, 

sediment transport, and bank erosion. Some research is 

being pursued to integrate the two scales of models 

(Colorado climate study special section on p. 48, for 

example); however, much work still remains to develop 

rigorous models linking basin- and channel-scale processes to stream habitat.

Basin-Scale Models

The link between land-use changes and hydrologic 

responses is addressed by many rainfall-runoff models. 

The models range in complexity from statistical representations—like regional flood frequency models—to 

spatially distributed, physically based models that 

account for rainfall, evapotranspiration, infiltration 

rates, soil moisture storage, variable-source area runoff 

production, and channel routing.

Effects of land-use changes can be explored and quantified in basin-scale models by changing factors such as 

evapotranspiration (as a function of land cover) or infiltration and storage (as functions of factors such as 

impermeable area, soil compaction, and impoundments). Two examples of this type of hydrologic model 

are the Precipitation-Runoff Modeling System 

(Leavesly and others, 1983) and the Hydrologic Simulation Program-FORTRAN (Bicknell and others, 

1993). In most cases, the ability of a model to predict 

changes in runoff and hydrograph timing is dependent 

on the calibration of some model parameters with measured data sets. Because models commonly cannot be 

calibrated under the conditions that are of interest—for 

example, future land-use changes—considerable uncertainty in the model predictions exist. Confidence in 

model predictions increases with the degree to which 

the model can represent realistic physical processes and 

the range of conditions over which it has been calibrated.

Sediment transport models traditionally have been 

more difficult to formulate and less reliable than hydrologic models. Statistical approaches to soil erosion 

models dominated the field for many years in the form 

of the USLE and variants (Wischmeier and Smith, 

1978). The statistical approach of the USLE provided 

useful predictions of soil erosion from field-size plots 

without requiring rigorous modeling of the hydrologic, 

erosion, and sediment transport processes that contribute to soil erosion. More recently, physically based 

models have begun to compete with the USLE 

approach. The dominant model is the Water Energy Prediction Project (WEPP) model (Lane and Nearing, 

1989). The WEPP model is based more on the physical 

representation of the hydrologic, soil erosion, and sediment transport processes than the USLE. Consequently, 

the WEPP model is considerably more complex and 

requires more data. In either type of model, the effects 

of land-use changes on soil erosion in a drainage basin 

can be simulated by changing parameters related to soil 

erodibility and vegetation characteristics.

Once runoff or sediment is simulated at the hill-slope 

scale in a model, it needs to be routed to a channel 

before its effects on instream habitat can be evaluated. 

Hydrograph routing through impoundments, structures, 

and channels typically is included in distributed hydrologic models; hydrograph routing requires additional 

data for channel characteristics, but the theory and 

application are well established. 

In contrast, sediment routing is not as well understood 

in theory or in practice. In fact, sediment routing is considered one of the most complex and challenging problems in geomorphology (Wolman, 1977). At the hillslope scale, the mass of soil delivered to adjacent channels can be related to the mass of soil eroded by empirical sediment delivery ratios. Sediment delivery ratios 

are known to vary with drainage area and basin characteristics, but the mechanical basis for determination of 

sediment delivery ratios is poorly understood (review in 

Walling, 1983). Once delivered to the stream channel, 

sediment typically does not move conservatively with 

water through fluvial systems. Instead, sediment can be 

deposited on the channel beds, banks, and bars and 

remain in storage for highly variable intervals before 

being remobilized and continuing its downstream travel 

(Meade and others, 1990). Recent advances in computational models of sediment routing have focused on 
INVESTIGATING THE LINKS BETWEEN LAND-USE AND PHYSICAL STREAM-HABITAT CHANGES 47

delivery of sediment from slopes to the channel and 

routing of fine, dominantly suspended-load sediment in 

relatively small drainage basins (Walling, 1983; Arnold 

and others, 1995). These models emphasize delivery of 

sediment to a basin outlet as a measure of offsite effects 

rather than evaluating the effects of sediment delivery 

and storage along the channel within the basin. Little 

emphasis has been placed in these computational models on sediment movement and routing within drainage 

basins or at scales where the sediment can affect stream 

habitats.

Channel-Scale Models

Links between water discharge variations and physical 

habitat availability in a channel reach are often estimated using hydraulic flow modeling. Physical habitat 

simulation was developed as a component of the 

Instream Flow Incremental Methodology (IFIM) 

(Bovee, 1982). The IFIM predicts the effects of incremental changes in streamflow on channel structure, 

water quality, temperature, and habitat availability by 

using a series of models. The physical habitat component (PHABSIM) of IFIM is a one-dimensional flow 

model that predicts usable habitat areas based on water 

discharge and fish habitat preferences (Bovee, 1982). 

This type of modeling approach is used to predict the 

effects of water diversions, dams, engineering structures, and changes in water release schedules on habitat 

availability for a selected species or habitat-use guild.

Modeling approaches, such as PHABSIM, require a 

variety of data to set up, calibrate, verify, and analyze 

the model prior to its use as a management or planning 

tool. Data required to use the model include reach 

topography and channel roughness characteristics, and 

calibration data consisting of water-surface elevations, 

velocities, and depths at multiple cross sections in a 

reach for one or more discharges. In addition, habitatuse data are needed to build habitat suitability curves 

for the species of interest. From these data, PHABSIM 

calculates a weighted usable habitat area at given discharges for a selected fish species or group of species. 

Habitat predictions can then be analyzed in terms of the 

time domain by considering the percentage of time habitat conditions exist during an average year or the probability that critical habitat conditions will exist during a 

specific time of the year, such as a spawning season.

Predictions from PHABSIM, and the PHABSIM procedure, have been questioned because of weak relations 

between predicted weighted usable habitat area and fish 

population size. Researchers have questioned whether 

fish sampling can define useful statistical models relating habitat to populations, and whether it should be 

expected that stream biota will use habitat in proportion 

to its availability (Orth, 1987; Zorn and Seebach, 1995). 

Biologic responses to changes in instream flows may 

include the effects of changes in food availability and 

distribution, water quality, temperature, and biotic 

interactions as well as physical habitat. Generally these 

biotic and chemical effects are not included in hydraulic 

simulations of habitat availability (Orth, 1987). In addition, weak relations between predicted and actual conditions have been attributed in part to low quality of the 

underlying hydraulic models. Hydraulic models in habitat simulation have been criticized because of the low 

spatial resolution of one-dimensional model formulations (Leclerc and others, 1995); because of dynamic 

channel instability that alters channel morphology during a flood hydrograph (Kondolf and Sale, 1985); and 

because variation in cross-section characteristics is not 

captured realistically in the models (Williams, 1996).

Because of these concerns with conventional hydraulic 

habitat analyses, other approaches to instream flow 

modeling are being studied (fig. 20). Two-dimensional 

hydraulic models, which have higher spatial resolution, 

have been proposed to improve predictions of depth and 

velocity responses to instream flow changes (Leclerc 

and others, 1995). Two additional analytical approaches 

have been proposed for the linkage of channel hydraulics with biologic responses. Latka and others (1993) 

avoid the issue of biological responses by comparing 

the distributions of channel depths and velocities with 

discharge scenarios to a historically defined hydraulic 

reference state. The underlying assumption in this 

approach is that the historical reference state had an 

optimal spatial and temporal distribution of habitats for 

native stream species. Another variation on the traditional instream flow approach is to assign discrete 

ranges of depth and velocity to particular macrohabitat 

types. The biological value of these habitat types would 

be determined from independent knowledge of critical 

habitat use by particular species. For example, behavioral studies of spawning might independently define a 

preferred depth and velocity range for a species of concern. The modeling analysis, then, would focus on the 
Previous studies have indicated that changes 

in climate may affect the timing and supply 

of water to riverine systems, but few studies 

have attempted to assess the effect of these 

changes on streamflow dependent processes. 

The USGS, in cooperation with the Colorado 

Water Conservation District, the Upper Gunnison River Water Conservancy District, 

Bureau of Reclamation, Bureau of Land 

Management, and National Park Service, used 

a series of process models to predict channel response to climate 

change in the East River, a tributary of the Gunnison River, in westcentral Colorado. The effects of changes in climate on bed-sediment 

flux were simulated by linking a watershed model (Leavesly and others, 

1983), a one-dimensional hydraulic model, and a sediment-transport relation (Parker and others, 1982). Using 

these models, hydrologic changes at the drainage-basin scale have been linked to channel hydraulics, which, in 

turn, are linked to sediment transporting events—the events that alter physical habitat.

The East River (drainage area 748 square kilometers) is a major contributor of streamflow to the Gunnison River 

in western Colorado. The basin elevations range from 2,440 to 4,359 meters and the mean monthly air 

temperatures range from less than -10o Celsius in January to almost 13o Celsius in July. Precipitation ranges from 

25 to almost 60 millimeters per month with the highest levels in November through March (mainly snowfall). 

Streamflow starts to increase in April with peak discharges in late May to early June due to snowmelt. The 

streambed substrate is cobble with a mean diameter of 112 millimeters for the surficial material and has a 

channel slope of 0.0048. The bankfull discharge at the gaging station at Almont, Colorado, is 89.2 cubic meters per 

second with a channel width of 25.9 meters and a mean depth of 1.58 meters.

. 

The East River is a major contributor of streamflow to 

the Gunnison River in western Colorado. Using data 

collected by the U.S. Geological Survey and climatological data, the effects of three air temperature values 

were modeled for a reach of the East River. Photograph 

courtesy of R.S. Parker, U.S. Geological Survey.

Gunnison River

Colorado River

East River

Grand Junction

COLORADO

0

0 50 MILES

50 KILOMETERS

Map Area

COLORADO

Climate Change Effects on Sediment and Streamflow—

Colorado

48
Most studies use streamflow volumes to 

evaluate the effects of climate change 

on water resources and often overlook 

streamflow-dependent issues such as 

channel maintenance, habitat, and 

sediment transport. In this study, a 

pebble size count technique was used to 

determine size distribution of the bed 

material. Photograph courtesy of R.S. 

Parker, U.S. Geological Survey.

Using data from October 1993 through September 1994, the effects of three mean annual air temperature values 

(2, 4, and 6o Celsius) were modeled for a reach of the East River. These increases in air temperature altered the 

timing of the streamflow hydrograph and reduced the annual streamflow volume by only 2, 5, and 7 percent. The 

changes in the timing of the streamflow hydrograph had a substantial effect on the bed-sediment discharge for 

the reach, however. The sediment flux was reduced by 86 percent for a 6o Celsius increase in air temperature.

Using linked models to simulate the effect of drainage-basin scale events on reach hydraulics and habitat 

maintenance provides a valuable tool to predict habitat responses to climate changes or other hydrologic 

disturbances. Although extension of such models to uncalibrated and unverifiable conditions can yield unreliable 

results, the models can provide essential insights into the operations of complex fluvial systems. In particular, 

such models can be used to explore tradeoffs and sensitivities among variables that govern runoff, sediment 

yield, and sediment transport.

For more information refer to Leavesly and others (1983) and Parker and others (1997).

49
Depth, velocity, and bed-material 

data are collected along transects 

on the Shenandoah River to 

calibrate the hydraulic part of the 

Physical HABitat SIMulation 

(PHABSIM) model. Photographs 

courtesy of D.C. Hayes, U.S. 

Geological Survey. 

Instream flow methodologies are useful to quantify 

habitat as a function of water discharge. Concerns 

have been raised that flow diversions from the 

Shenandoah River, Virginia, for public-water 

supply may decrease habitat volumes available 

for fish. The USGS is working cooperatively 

with the Lord Fairfax Planning District Commission, 

Virginia Polytechnic University, Virginia Department of Game and 

Inland Fisheries, and the U.S. Army Corps of Engineers to evaluate 

minimum streamflows necessary to maintain fish habitat in the 

Shenandoah River. The study is using the PHABSIM model to quantify 

the areal extent of depth and velocity in the stream channel for a range 

of discharges.

Representative reaches for instream flow modeling were selected based on a basinwide overview of hydrologic, 

geologic, and soils data. The mainstem of the Shenandoah River has three distinct segments: the upper segment 

of mostly long pools and short riffles, the middle segment similar to the upper segment with the additional 

features of islands and bends, and the lower segment, which has longer and wider riffles than the other 

segments.

A reach in the middle segment was selected for modeling in a demonstration project (Zappia and Hayes, 1998). 

Twenty-one cross sections were laid out to determine the variability in macrohabitats and to define hydraulic 

controls. Stage, velocity, and depth data were collected at three different discharges for use in calibration and 

verification of the hydraulic model. Bed-material particle-size data were collected to help estimate hydraulic 

roughness coefficients.

Once calibrated and verified, the hydraulic model results were merged in the PHABSIM model with fish 

distribution information selected from previously published reports. Fish species were classified into habitat 

preference guilds to minimize variations due to nonphysical causes. Habitat suitability curves were compared 

with the hydraulically based model to illustrate habitat availability at various discharges and to estimate the 

biological effect of low flows. 

The Shenandoah River, Virginia, is dominated by 

riffle and run habitats. Studies are intended to 

evaluate how fish populations in these habitats 

would be affected by decreases in streamflow.

Shenandoah River

Potomac River

Rappahannock R

Washington

0

0 50 MILES

50 KILOMETERS

DC

VIRGINIA

WEST

VIRGINIA

MD

VIRGINIA

Map Area

Minimum Instream Flow Modeling—Virginia and Washington

50
Similar studies have been carried out by the 

USGS in cooperation with the Stillaquamish 

Indian Tribe, Pierre County Department of 

Public Works, and the State of Washington 

Department of Ecology in the Pacific Northwest, 

where maintaining flows for salmonid habitats 

is of great concern (Embrey, 1987; 1991). These 

studies underscore the point that different flows are 

necessary at different times of the year to optimize habitat 

for particular species and life stages. For example, on the 

South Fork Stillaguamish River, Washington, optimization of 

discharge for spawning of Steelhead would require discharges 

that would minimize available habitat for Steelhead fry.

For more information refer to Bovee (1982), Embrey 

(1987, 1991), Leclerc and others (1995), Zappia and 

Hayes (1998), and Williams (1996) or contact District 

Chief, U.S. Geological Survey, 3600 West Broad Street, 

Richmond, VA 23230.

Results from instream flow modeling in Washington 

State show the availability of habitat for a variety of fish 

species and life stages as a function of discharge. On the 

South Fork Stillaguamish River, flows that optimize 

habitat for some life stages and species provide minimal 

habitat for other life stages and species. On regulated 

rivers, managers can use this type of information to 

design complex seasonal release patterns to optimize 

benefits to all species.

0

20,000

40,000

60,000

80,000

100,000

Measured discharge

Coho juvenile

Chinook fry

Steelhead juvenile

Steelhead fry

Steelhead

adult

Steelhead

spawning

Pink spawning

Chum spawning

Chinook spawning

0 1,000 2,000 3,000 4,000

DISCHARGE, IN CUBIC FEET PER SECOND

HABITAT, IN SQUARE FEET PER 1000 FEET OF STREAM

WASHINGTON

Map Area

Stillaguamish R

Puget

Sound

Everett

Bellingham

0

0 50 MILES

50 KILOMETERS

WASHINGTON

CANADA

51
52 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

 

1991

ELEVATION, IN METERS ABOVE

ARBITRARY DATUM

1994

EXPLANATION

99.0

98.5

98.0

97.5

97.0

96.5

96.0

95.5

95.0

94.5

94.0

93.5

93.0

0.125 0.250 MILES

0.125

0

0

1991 Channel 1994 Channel

1,000

2,000

3,000

4,000

5,000

6,000

7,000

AREA, IN SQUARE METERS

0

VELOCITY, IN METERS PER SECOND

0 DEPTH, IN METERS

0

1

2

3

4

2.0 2.4 0.8 1.2 1.6 0.4 2.0 2.4 0.8 1.2 1.6 0.4

0.250 KIL0METERS

Figure 20. Example of using a two-dimensional hydraulic model to determine areal distributions of velocity 

and depth pairs for an entire reach, same bankfull discharge, for two different channel configurations. This 

example is from a small stream (about 700 square-kilometers drainage area) in the Missouri Ozarks. 

Between the 1993 topographic survey and the 1994 topographic survey, the channel was subjected to about 

a 50-year recurrence-interval flood. The maps show the topographic mesh and the graphs (bottom) show 

modeled areal distributions of depth and velocity for the two cases. The 1994 channel shows greater 

hydraulic diversity as indicated by the spread of depth and velocity distribution.
LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS 53

spatial and temporal distribution of the spawning macrohabitat patch rather than on predictions of fish populations (Bovee and others, 1997). This approach avoids 

difficult considerations of biotic responses while adding 

the ability to explicitly analyze the spatial organization 

of macrohabitat patches within a reach.

Hydraulic habitat simulation models commonly assume 

that the channel bed and banks are stable during the 

time interval of interest. This assumption frequently is 

violated in channels with sand-size and smaller bed 

material in which bedload transport can change channel 

morphology substantially during an individual flood. 

Recent developments of models that incorporate sediment erosion and transport and bank erosion promise to 

increase understanding of habitat stability and change 

in dynamic channels. Wiele and others (1996) presented 

such a model to investigate changes in channel morphology resulting from the design flood on the Colorado River. This model included sediment transport and 

deposition and demonstrated that computational models could predict channel changes at a scale applicable 

to fish habitat.

LAND-USE CHANGES AND THE PHYSICAL HABITAT 

OF STREAMS

Physical stream habitat is defined by the water temperature, turbidity, depth, velocity, bed material, and cover 

in which stream organisms live. Stream habitat is 

thought to be a first-order determinant of stream ecosystem structure and functioning because it defines the 

physical spaces within which organisms use stream 

resources. Resource partitioning theories and empirical 

studies of distributions of stream organisms among habitats support the importance of physical habitat in determining ecosystem structure. Water-column chemical 

characteristics can have an equal or greater effect on 

stream ecosystems by defining a chemical habitat, 

depending on chemical concentrations and constituents. Physical habitat changes can affect ecosystems 

either independent of water-column effects or in concert with them. Hence, physical stream habitat should 

be evaluated to determine the cause-and-effect links 

between suspected environmental stressors and biological characteristics. In general, physical-habitat changes 

are more persistent and more pervasive than chemicalhabitat changes. Together, physical and chemical habitats define the template of which within potential biotic 

interactions—such as predation and competition—act 

to determine details of ecosystem structure.

Many land-use changes have the potential to alter 

stream channels and physical stream habitat by changing rates and mechanisms of channel-forming processes. The realization of potential depends on the magnitude and characteristics of the land-use change, where 

it occurs on the landscape, and, in many cases, the history and subsequent sequence of climatic and land-use 

events. Determination of whether a change has 

occurred or is occurring can itself be problematic 

because of the spatial and temporal variability within 

fluvial systems. To identify habitat disturbance due to 

land-use changes requires quantifying the natural variability of streams in dynamic equilibrium so conditions 

of nonequilibrium (disturbance) can be identified.

The fluvial systems within which land-use changes are 

transmitted to stream habitats can respond to disturbances with lags, thresholds, and cumulative responses. 

As a result, disturbances may affect sites far removed 

from where they originated and, at times, long after they 

occurred. Discerning the links between land-use 

changes and stream habitats is easier for direct disturbances in the riparian zone than for diffuse land-use 

changes throughout a drainage basin. The “complex 

response” of fluvial systems presents a challenge to predictive models.

Within the spatial and temporal variability of these factors, valid generalizations of how land-use changes will 

affect stream habitats can be difficult to make. As stated 

by Leopold (1994): “The river responds to physics, but 

there remains much latitude in the morphology that a 

channel may assume.” There is even greater latitude 

when considering channel characteristics at the macrohabitat scale. In many cases, unique combinations of 

land-use change, climate, geology, or biological interactions will result in unique metamorphosis of the channel and associated habitats.

Land-use changes generally can be placed into two categories: those that affect uplands and those that affect 

the channel or riparian zone directly (table 1). Upland 

land-use practices can be further categorized into those 

that affect runoff characteristics (quantity and timing) 

and those that affect sediment yield. Runoff and sedi-
54 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

ment yield are not independent, yet they often change at 

different rates depending on the type of land-use 

change. It is, therefore, useful to consider the effects 

separately.

The response of channel reaches to land-use changes in 

the uplands can be conditioned by lags, thresholds, and 

cumulative effects. The slow and episodic routing of 

sediment from upland disturbances can cause channel 

and habitat changes in a downstream reach at a time far 

after the initial disturbance. Internal thresholds can 

result in nonlinear responses when the threshold is 

overcome. Wave-like movement of sediment in drainage networks can result in downstream increases in 

channel and habitat instability.

Unlike the complexities inherent with routing runoff 

and sediment from upland disturbances, those disturbances that occur in or adjacent to the channel are more 

easily associated with physical habitat responses. In 

many cases, however, land-use changes in the riparian 

zone occur at the same time as changes in the uplands. 

In these cases, a primary consideration may be to determine the relative magnitude of the effects so monitoring 

or policy can be most effectively applied.

Changes in the riparian zone that affect physical stream 

habitat can be classified into four general types (table 

1): those that alter discharge and sediment yield at 

points in the stream network (usually dams, diversions, 

or outfalls); those that alter channel slope or cross-sectional morphology directly; those that alter hydraulic 

flow resistance; and those that alter erosional resistance 

of the bed or banks.

For any particular riparian land-use change, one or 

more of these types might apply. For example, common 

stream channelization practices involve simultaneous 

decreases in flow resistance provided by riparian vegetation, decreases in bank erosional resistance, and direct 

changes in channel slope and cross-sectional morphology. Responses from one riparian land-use change may 

also progress from one type to another. For example, an 

instream gravel-mining operation may only take gravel 

from the bed of a stream, thereby increasing local slope 

and initiating channel degradation. Channel degradation, however, may oversteepen banks, resulting in bank 

instability and decreased flow and erosional resistance.

Diagnosis of the links between land use and habitat 

change can require multifaceted, multiscale, and multidisciplinary approaches. In some cases, simple hydrologic and nonpoint-source sediment models can provide 

insight sufficient to determine if particular land-use 

changes have the potential to substantially alter runoff 

and sediment yield. However, computational models do 

not typically include time frames and realistic representations of sediment routing or channel-scale processes 

necessary to determine the effects on stream habitats. 

Improved understanding of the links between land-use 

changes and stream habitats likely will require a combination of historical, associative, process-scale, and 

modeling approaches.
LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS 55

Table 1. Typical channel habitat responses to changes in land use in upland and riparian areas

[LWD, large woody debris. Channel and habitat responses are typical and assume that only one factor has changed. In reality, most fluvial systems will be characterized 

by simultaneous changes of two or more factors, thereby complicating prediction of responses. Riparian areas encompass the land in and adjacent to the stream channel. 

Land uses in the riparian areas include direct effects on the channel (such as impoundments and channelization) and on the adjacent bars, banks, and flood plain. Embeddedness is a measure of the extent to which the interstices of bed material are filled with finer sediment.]

Location Factor Typical land-use examples Typical effects on channel 

and habitat Complications and interactions

Upland 

areas

Runoff 

increase

Urbanization, agriculture, or forestry practices can increase 

annual runoff volume and/or peak 

discharge.

Increase in channel cross sectional 

area, flood disturbance, LWD 

recruitment, and connections with 

flood plain; decrease in drought 

disturbance, embeddedness, 

cover, and LWD retention; widthto-depth ratio changes dependent 

on particle sizes of bedload, bed, 

and banks.

Interactions with sediment load 

are critical to morphology 

changes. Cumulative effects 

downstream affected as well by 

contributions of other land uses, 

channel network effects on flow 

routing, and riparian effects on 

flow routing. 

Runoff

decrease

Fire suppression, exotic vegetation encroachment, and detention 

ponds can decrease annual runoff 

by increasing evapotranspiration 

and infiltration, perhaps decreasing peak discharge.

Decrease in channel cross sectional area, flood disturbance, 

LWD recruitment, and connections 

with flood plain; increase in 

drought disturbance, embeddedness, cover, and LWD retention; 

width-to-depth ratio changes 

dependent on particle sizes of 

bedload, bed, and banks.

Sediment 

yield

increase

Urbanization, agriculture, forestry, or mining can increase soil 

erosion and sediment yield above 

natural levels.

Decrease in channel cross sectional area; increase in sedimentation disturbance, embeddedness, 

cover, LWD retention, and connections with flood plain; width-todepth ratio changes dependent on 

particle sizes of sediment load, 

bed, and banks.

Sediment does not route immediately to streams. Storage and 

lagged remobilization may complicate channel and habitat 

response. Sediment routed 

through channel networks may 

increase in volume or diminish 

downstream. Sediment yield 

changes may interact with 

changes in runoff to determine 

channel and habitat responses. 

Increased sediment yield may trigger channel instability.

Sediment 

yield 

decrease

Fire suppression, exotic vegetation, or small impoundments that 

trap sediment can result in sediment yield that is less than that of 

natural landscape.

Increase in channel cross sectional 

area; decrease in sedimentation 

disturbance, embeddedness, 

cover, LWD retention, and connections with flood plain; width-todepth ratio changes dependent on 

particle sizes of sediment load, 

bed, and banks.

Table 1 continues on the next page.
56 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

Riparian 

areas

Discharge 

increase

Augmentation from diverted flow 

from other basins or irrigation 

return flow can increase mean 

annual runoff; seasonal timing is 

likely to differ from natural condition; discharge timing changed.

Increase in channel cross-sectional area, flood disturbance, 

LWD recruitment, connections 

with flood plain. Decrease in 

drought disturbance, embeddedness, cover, LWD retention. Widthto-depth ratio changes dependent 

on particle size of bedload, bed, 

and banks.

Sediment loads downstream of 

dams are typically diminished, 

and those contributed by augmented discharge are likely to be 

low; therefore, sediment deficits 

will tend to me more sever than 

case of increased runoff alone. 

Interactions with sediment load 

are critical to morphology 

changes. Cumulative downstream 

effects influenced as well by contributions of other land uses, 

channel network effects on flow 

routing, and riparian effects on 

flow routing.

Discharge

decrease

Diversions, irrigation, reservoirs, 

and encroachment of phreatophyte vegetation can decrease 

mean annual discharge; seasonal 

timing is likely to differ from that 

of natural condition, see discharge 

timing change below.

Decrease in channel cross sectional area, flood disturbance, 

LWD recruitment, and connections 

with flood plain; increase in 

drought disturbance, embeddedness, cover, LWD retention; widthto-depth ratio changes dependent 

on particle sizes of bedload, bed, 

and bank.

Discharge 

timing 

change

Diversion, irrigation, and reservoirs typically change seasonal 

patterns of discharge, increase 

base flow, and decrease peak flow.

Same as above, plus alterations of 

seasonal availability of habitats.

Effects of prolonged base flows 

below bed-sediment-transport 

thresholds on channel morphology are uncertain. Effects of peaking releases on channel habitats 

are poorly quantified.

Sediment 

yield 

increase

Instream aggregate mining, 

urbanization, agriculture, or forestry practices in the riparian zone 

can increase sediment yields 

directly to stream reaches.

Decrease in channel cross sectional area; increase in sedimentation disturbance, embeddedness, 

cover, LWD retention, and connections with flood plain; width-todepth ratio changes dependent on 

particle sizes of sediment load, 

bed, and banks.

Sediment routes immediately to 

adjacent, downstream segments. 

Additional downstream routing 

must account for storage and lags. 

Sediment routed through channel 

networks may increase in volume 

or diminish downstream. Sediment increases may interact with 

changes in runoff to determine 

channel and habitat responses. 

Fine sediment additions during 

low flow have greater effect on 

substrate conditions than the 

same sediment yield during natural floods.

Sediment 

yield 

decrease

Reservoirs, dredging, and 

instream aggregate mining 

(coarse sediment) can reduce sediment load of the river.

Increase in channel cross sectional 

area; decrease in sedimentation 

disturbance, embeddedness, 

cover, LWD retention, connections 

with flood plain. Width-to-depth 

ratio changes dependent on particle sizes of sediment load, bed, 

and banks.

Decrease in sediment load is 

transmitted directly to the channel. Bed degradation due to 

decreased sediment load may 

extend both upstream and downstream from the site of disturbance. Decreases in sediment load 

often are associated with 

decreases in peak flows due to 

reservoir regulation leading to 

complex channel and habitat 

responses.

Table 1 continues on the next page.

Table 1. Typical channel habitat responses to changes in land use in upland and riparian areas

[LWD, large woody debris. Channel and habitat responses are typical and assume that only one factor has changed. In reality, most fluvial systems will be characterized 

by simultaneous changes of two or more factors, thereby complicating prediction of responses. Riparian areas encompass the land in and adjacent to the stream channel. 

Land uses in the riparian areas include direct effects on the channel (such as impoundments and channelization) and on the adjacent bars, banks, and flood plain. Embeddedness is a measure of the extent to which the interstices of bed material are filled with finer sediment.]

Location Factor Typical land-use examples Typical effects on channel 

and habitat Complications and interactions
LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS 57

Riparian 

areas

Slope 

increase

Channelization and instream 

aggregate mining can increase 

local channel slopes.

Channel incision leads to bank and 

bed instability; straightened 

reaches recover by increasing sinuosity. Increase in channel cross 

sectional area; decrease in sedimentation disturbance, embeddedness, cover, LWD retention, 

connections with flood plain; initial decrease in width-to-depth 

ratio, but ultimate changes dependent on particle sizes of sediment 

load, bed, and banks.

Response to channelization and 

instream mining can extend up 

and downstream. Bank erosion 

processes are instrumental in 

determining rates and processes 

of recovery.

Crosssectional 

area 

increase

Channelization and instream 

aggregate mining can increase 

channel cross-sectional areas by 

direct excavation.

Initial disturbance determines 

channel morphology, decreases 

LWD retention, and can have variable effects on bed material.

Responses to direct channel 

change and recovery may be rapid 

and interrelated with slope and 

hydraulic resistance.

Crosssectional 

area 

decrease

Levees and navigation structures 

can decrease floodway and channel cross-sectional area.

Decrease in channel cross section 

area, width-to-depth ratio, LWD 

retention, connection to flood 

plain, cover, embeddedness, and 

sedimentation disturbance; generally decrease in hydraulic diversity.

Decreased channel migration 

tends to decrease lateral disturbance, whereas greater depths 

increase basal shear stresses and 

bed disturbance. Decreased diversity of main channel may be compensated by new, but different, 

habitats associated with structures.

Flow 

resistance 

increase

Vegetation encroachment on the 

channel can increase flow resistance.

Decrease in channel cross sectional area, embeddedness, widthto-depth ratio. Increase in depth, 

sedimentation disturbance on 

margins, cover, LWD retention, 

connections with flood plain.

Vegetation interactions with flow 

depend on stem density, crosssectional area presented to flow, 

where vegetation is in flow field, 

and extent to which it bends. Vegetation effects also vary with community age and structure. May 

decrease disturbance associated 

with channel migration.

Flow 

resistance 

decrease

Bank revetments, channelized 

streams, and clearing of riparian 

areas for agriculture or forestry 

can decrease hydraulic flow resistance in channel and flood plain.

Increase in channel cross sectional 

area, width-to-depth ratio, embeddedness, disturbance; decrease in 

cover, LWD retention.

Decrease in flow resistance can be 

permanent (for example, concrete 

channel bed and banks) or temporary (from clearing LWD). Temporary changes will involve transient 

responses as channel and riparian 

vegetation adjust.

Erosion 

resistance 

increase

Revetments and vegetation 

encroachment can increase the 

strength of banks and bed to resist 

erosion.

If banks are strengthened, but bed 

is not, then depth will increase in 

and width-to-depth ratio will 

decrease; if bed is strengthened 

but banks are not (for example, 

grade-control structures), then 

opposite is likely; decrease in disturbance from channel migration, 

embeddedness, and LWD loading. Increase in bed-scour disturbance, and cover.

Erosional resistance interacts with 

flow resistance and channel morphology. Bank stabilization measures to increase erosion 

resistance in one reach can result 

in lowered flow resistance and 

consequent transmission of 

energy downstream.

Erosion 

resistance 

decrease

Urbanization, agriculture, and forestry can decrease erosional resistance of bed and banks.Increase in width, width-to-depth 

ratio, disturbance, and LWD loading. Decrease in cover.

Decreases in bank erosion resistance are subject to thresholds as 

banks go from convex to concave 

upward. Steep and high banks 

have minimal strength contributed 

by vegetation.

Table 1. Typical channel habitat responses to changes in land use in upland and riparian areas

[LWD, large woody debris. Channel and habitat responses are typical and assume that only one factor has changed. In reality, most fluvial systems will be characterized 

by simultaneous changes of two or more factors, thereby complicating prediction of responses. Riparian areas encompass the land in and adjacent to the stream channel. 

Land uses in the riparian areas include direct effects on the channel (such as impoundments and channelization) and on the adjacent bars, banks, and flood plain. Embeddedness is a measure of the extent to which the interstices of bed material are filled with finer sediment.]

Location Factor Typical land-use examples Typical effects on channel 

and habitat Complications and interactions
58 LAND-USE CHANGES AND THE PHYSICAL HABITAT OF STREAMS

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Jacobson, Femmer, and McKenney—Land-Use Changes and the Physical Habitat of Streams—Circular 1175