U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2006-5025

Prepared in cooperation with the Northern Shenandoah Valley Regional Commission

Physical Habitat Classification and Instream

Flow Modeling to Determine Habitat Availability

During Low-Flow Periods, North Fork

Shenandoah River, Virginia
Cover photograph (left) of the upper section of the North Fork Shenandoah River near Cootes Store, Virginia, by 

Jennifer L. Krstolic, U.S. Geological Survey, October 15, 2002. Cover photograph (center) of the middle section 

of the North Fork Shenandoah River near Mount Jackson, Virginia, by Donald C. Hayes, U.S. Geological Survey, 

October 10, 2001. Cover photograph (right) of the lower section of the North Fork Shenandoah River near mouth, 

by Donald C. Hayes, U.S. Geological Survey, October 10, 2001.
Physical Habitat Classification and Instream

Flow Modeling to Determine Habitat Availability

During Low-Flow Periods, North Fork

Shenandoah River, Virginia

By Jennifer L. Krstolic, Donald C. Hayes, and Peter M. Ruhl

Prepared in cooperation with the Northern Shenandoah Valley Regional Commission

Scientific Investigations Report 2006–5025

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

U.S. Geological Survey, Reston, Virginia: 2006

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

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Denver, CO 80225

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Information about water resources in Virginia is available online at http://va.water.usgs.gov

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U.S. Government.

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reproduce any copyrighted materials contained within this report.

Suggested Citation:

Krstolic, J.L., Hayes, D.C., and Ruhl, P.M., 2006, Physical Habitat Classification and Instream Flow Modeling to

Determine Habitat Availability During Low-Flow Periods, North Fork Shenandoah River, Virginia: U.S. Geological

Survey Scientific Investigations Report 2006-5025, 63 p.
iii

Contents

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

Introduction ................................................................................................ 2

Purpose and Scope ................................................................................. 4

Hydrogeology ....................................................................................... 4

Analysis of Historic Streamflow Data .................................................................. 6

Habitat Classification .................................................................................... 14

Mesohabitat Classification ........................................................................ 14

Methods ....................................................................................... 14

Results ....................................................................................... 16

Hydraulic Data Collection in the Predominant Mesohabitat Types ........................... 19

Selection of Reaches ........................................................................ 19

Description of Reaches and Transects ................................................... 19

Hydraulic Data Collection Methods ...................................................... 19

Fish-Community Sampling and Microhabitat Observations .................................... 21

Community Sampling ........................................................................ 21

Microhabitat Observations .................................................................. 21

Development of Fish Habitat-Suitability Curves ................................................ 24

Canoeing Suitability Curves ..................................................................... 24

Instream Flow Modeling to Determine Fish Habitat Availability .................................... 24

Model Calibration ................................................................................. 24

Inputs .......................................................................................... 24

Water-Surface Elevation Calibration ...................................................... 24

Velocity Calibration ........................................................................... 28

Habitat Simulation and Development of Weighted Usable-Habitat Area Curves ......... 28

Habitat-Discharge Relations for the Management Sections ................................. 31

Upper Section ................................................................................. 31

Middle Section .............................................................................. 38

Lower Section ................................................................................. 38

Time-Series Analysis for Low-Flow Periods ................................................... 39

Summary and Conclusions .............................................................................. 46

Acknowledgments ....................................................................................... 48

References Cited .......................................................................................... 48

Appendix 1. RHABSIM Model-Calibration Data from the Hydraulic

Data-Collection Reaches ........................................................................ 51
iv

Figures

 1–2. Maps showing:

1. Location of the North Fork Shenandoah River Basin, Virginia (study area). ............ 3

2. Upper, middle, and lower management sections, location of

study reaches, and topography in the North Fork Shenandoah

River Basin, Virginia. .......................................................................................................... 5

3–18. Graphs showing:

 3. Annual and seasonal flow-duration curves for three

streamflow-gaging stations on the North Fork Shenandoah

River, Virginia: at Cootes Store, Va. (01632000) (A); at Mount

Jackson, Va. (01633000) (B); near Strasburg, Va. (01634000) (C). ................................ 9

4. Number of days per summer month (July, August, September, and

October) for the years 1925–2002 with streamflow values equal to

or less than the 90-percent exceedance flow (1.6 cubic feet per

second) for the Cootes Store streamflow-gaging station (01632000)

on the North Fork Shenandoah River, Virginia. ............................................................ 11

5. Number of days per summer month (July, August, September,

and October) for the years 1943–2002 with streamflow values

less than the 90-percent exceedance flow (30 cubic feet per

second) for the Mount Jackson streamflow-gaging station

(0163300) on the North Fork Shenandoah River, Virginia. .............................................. 12

 6. Number of days per summer month (July, August, September,

and October) for the years 1925–2002 with streamflow values

less than the 90-percent exceedance flow (87 cubic feet per

second) for the Strasburg streamflow-gaging station

(0163400) on the North Fork Shenandoah River, Virginia. .............................................. 13

7. Cumulative length of riffle (A), run (B), and pool (C) mesohabitat

types in the upper, middle, and lower management sections

of the North Fork Shenandoah River, Virginia. River mile zero

represents the confluence of smaller tributaries to form the

headwaters of the North Fork Shenandoah River. ...................................................... 18

8. Fish habitat depth-suitability curves for riffle (A),

fast-generalist (B), pool-run (C), and pool-cover guilds (D),

and canoeing habitat depth-suitability curve (E) for the

North Fork Shenandoah River, Virginia. ........................................................................ 25

9. Fish habitat velocity-suitability curves for riffle (A),

fast-generalist (B), pool-run (C), and pool-cover guilds (D),

and canoeing habitat velocity-suitability curve (E) for the

North Fork Shenandoah River, Virginia. ........................................................................ 26

10. Fish habitat channel index-suitability curves for riffle (A),

fast-generalist (B), pool-run (C), and pool-cover fish guilds (D),

and canoeing habitat channel index-suitability curve (E) for

the North Fork Shenandoah River, Virginia. ................................................................. 27

11. Weighted usable-habitat area for the upper management

section of the North Fork Shenandoah River, Virginia. .............................................. 35

12. Weighted usable-habitat area for the middle management

section of the North Fork Shenandoah River, Virginia. .............................................. 36
v

13. Weighted usable-habitat area for the lower management

section of the North Fork Shenandoah River, Virginia. .............................................. 37

14. Daily mean discharge and weighted usable-habitat area

(WUA) for fish guilds in the upper management section 

of the North Fork Shenandoah River, Virginia for the

1930 low-flow period (A), 1964 low-flow period (B), and 1999

low-flow period (C). Discharge associated with the maximum

WUA for all fish guilds in this section of the river is indicated. ................................ 40

15. Daily mean discharge and weighted usable-habitat area

(WUA) for fish guilds in the middle management section 

of the North Fork Shenandoah River, Virginia for the 1964

low-flow period (A), 1999 low-flow period (B). Discharge

associated with the maximum WUA for all fish guilds in this

section of the river is indicated. ..................................................................................... 41

16. Daily mean discharge and weighted usable-habitat area

(WUA) for fish guilds in the lower management section 

of the North Fork Shenandoah River, Virginia for the 1930

low-flow period (A), 1964 low-flow period (B), and 1999 low-flow

period (C). Discharge associated with the maximum WUA for all

fish guilds in this section of the river is indicated. ...................................................... 42

17. Weighted usable-habitat area for the fast-generalist fish

guild under three different water-withdrawal scenarios

in 1999 in the upper management section of the North Fork

Shenandoah River, Virginia. ............................................................................................ 44

18. Weighted usable-habitat area for the pool-cover fish

guild under three different water-withdrawal scenarios

in 1999 in the lower management section of the North Fork

Shenandoah River, Virginia. ............................................................................................ 45

Tables

1. Continuous monitoring streamflow-gaging stations on the

North Fork Shenandoah River, Virginia. ................................................................................... 6

 2. Monthly, seasonal, and annual exceedance flows for three

streamflow-gaging stations on the North Fork Shenandoah

River, Virginia. ............................................................................................................................... 7

3. Average and maximum number of days in July, August, and

September that streamflows were equal to or less than specified

low-flow period exceedance values on the North Fork

Shenandoah River, Virginia. ..................................................................................................... 10

4. The number of days flows were equal to or less than the 90-percent

exceedance value for July, August, and September during dry

years on the North Fork Shenandoah River, Virginia. .......................................................... 14

5. Habitat type descriptions used for classification of mesohabitat on

the North Fork Shenandoah River, Virginia. .......................................................................... 15

6. Results of the mesohabitat classification and mapping for three

management sections of the North Fork Shenandoah River, Virginia. ............................. 17
vi

7. Locations of river reaches studied during hydraulic data collection

on the North Fork Shenandoah River, Virginia. ..................................................................... 19

8. Mesohabitat types represented by transects in the hydraulic datacollection reaches on the North Fork Shenandoah River, Virginia. .................................. 20

9. Best-estimate calibration discharges for each hydraulic datacollection reach on the North Fork Shenandoah River, Virginia. ...................................... 20

10. Species and guild classification for fish identified in the North

Fork Shenandoah River. ............................................................................................................ 22

11. Substrate codes used to classify the dominant and subdominant

substrate within fish study reaches and hydraulic data-collection

transects on the North Fork Shenandoah River, Virginia. ................................................... 23

12. Codes used to describe the cover found around a fish observation

site and within hydraulic data-collection transects on the North

Fork Shenandoah River, Virginia. ............................................................................................ 23

13. Codes used to classify the percentage of fine particulate matter

within a one square-meter area around a fish observation site

and within hydraulic data-collection transects on the North

Fork Shenandoah River, Virginia. ............................................................................................ 23

14. Water-surface calibration method used in RHABSIM for each

hydraulic data-collection reach on the North Fork Shenandoah

River, Virginia. ............................................................................................................................. 28

15. Simulation flows for the hydraulic data-collection reaches in the

upper, middle, and lower management sections of the North Fork

Shenandoah River, Virginia ...................................................................................................... 29

16. Drainage-area-based correction factors for relating discharge

measured at hydraulic data-collection reaches to discharge

measured at streamflow-gaging stations on the North Fork

Shenandoah River, Virginia. ..................................................................................................... 30

17. Velocity calibration discharges used in RHABSIM for each

hydraulic data-collection reach and transect on the North

Fork Shenandoah River, Virginia. ............................................................................................ 30

18. Weighted usable-habitat area in square feet per 1,000 feet

of stream for the upper management section of the North Fork

Shenandoah River, Virginia. ..................................................................................................... 32

19. Weighted usable-habitat area in square feet per 1,000 feet

of stream for the middle management section of the North Fork

Shenandoah River, Virginia. ..................................................................................................... 33

20. Weighted usable-habitat area in square feet per 1,000 feet of

stream for the lower management section of the North Fork

Shenandoah River, Virginia. ..................................................................................................... 34
vii

Conversion Factors and Datum 

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2)

acre 0.004047 square kilometer (km2)

square foot (mi2) 0.09290 square meter (m2)

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 

Volume

gallon (gal) 3.785 liter (L) 

gallon (gal) 0.003785 cubic meter (m3) 

million gallons (Mgal) 3,785 cubic meter (m3)

cubic foot (ft3) 0.02832 cubic meter (m3) 

Flow rate

foot per second (ft/s) 0.3048 meter per second (m/s)

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

cubic foot per second per square 

mile [(ft3/s)/mi2]

 0.01093 cubic meter per second per square 

kilometer [(m3/s)/km2]

million gallons per day (Mgal/d) 0.04381 cubic meter per second (m3/s)

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

 °F=(1.8×°C)+32

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

 °C=(°F-32)/1.8

Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27), 

unless otherwise noted in the text or figures. 

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88), unless otherwise noted in the text or figures.
viii

Abbreviations:

DEQ Virginia Department of Environmental Quality

GIS Geographic Information System

GPS Global Positioning System

HSC Habitat Suitability Criteria

IFIM Instream Flow Incremental Methodology

MANSQ Manning Stage-Discharge

NSVRC Northern Shenandoah Valley Regional Commission

NWIS National Water Inventory System

PHABSIM Physical Habitat Simulation Model

RHABSIM River Habitat Simulation Model

SFZ Stage of Zero Flow

SI Suitability Index

USGS U.S. Geological Survey

VAF Velocity Adjustment Factors

VPI Virginia Polytechnic Institute and State University

WSL Water-Surface Elevation

WSP Water-Surface Profile

WUA Weighted usable-habitat area
Abstract

Increasing development and increasing water withdrawals 

for public, industrial, and agricultural water supply threaten to 

reduce streamflows in the Shenandoah River basin in Virginia. 

Water managers need more information to balance human 

water-supply needs with the daily streamflows necessary for 

maintaining the aquatic ecosystems. To meet the need for 

comprehensive information on hydrology, water supply, and 

instream-flow requirements of the Shenandoah River basin, 

the U.S. Geological Survey and the Northern Shenandoah 

Valley Regional Commission conducted a cooperative investigation of habitat availability during low-flow periods on the 

North Fork Shenandoah River. 

 Historic streamflow data and empirical data on physical habitat, river hydraulics, fish community structure, and 

recreation were used to develop a physical habitat simulation model. Hydraulic measurements were made during low, 

medium, and high flows in six reaches at a total of 36 transects 

that included riffles, runs, and pools, and that had a variety of 

substrates and cover types. Habitat suitability criteria for fish 

were developed from detailed fish-community sampling and 

microhabitat observations. Fish were grouped into four guilds 

of species and life stages with similar habitat requirements. 

Simulated habitat was considered in the context of seasonal 

flow regimes to show the availability of flows that sustain suitable habitat during months when precipitation and streamflow 

are scarce. 

The North Fork Shenandoah River basin was divided 

into three management sections for analysis purposes: the 

upper section, middle section, and lower section. The months 

of July, August, and September were chosen to represent a 

low-flow period in the basin with low mean monthly flows, 

low precipitation, high temperatures, and high water withdrawals. Exceedance flows calculated from the combined data 

from these three months describe low-flow periods on the 

North Fork Shenandoah River. Long-term records from three 

streamflow-gaging stations were used to characterize the flow 

regime: North Fork Shenandoah River at Cootes Store, Va. 

(1925–2002), North Fork Shenandoah River at Mount Jackson, Va. (1943–2002), and North Fork Shenandoah River near 

Strasburg, Va. (1925–2002). 

The predominant mesohabitat types (14 percent riffle, 

67.3 percent run, and 18.7 percent pool) were classified along 

the entire river (100 miles) to assist in the selection of reaches 

for hydraulic and fish community data collection. The upper 

section has predominantly particle substrate, ranging in size 

from sand to boulders, and the shortest habitat units. The 

middle section is a transitional section with increased bedrock substrate and habitat unit length. The lower section has 

predominantly bedrock substrate and the longest habitat units 

in the river. 

The model simulations show that weighted usablehabitat area in the upper management section is highest at 

flows higher than the 25-percent exceedance flow for July, 

August, and September. During these three months, total 

weighted usable-habitat area in this section is often less than 

the simulated maximum weighted usable-habitat area. Habitat 

area in the middle management section is highest at flows 

between the 25- and 75-percent exceedance flows for July, 

August, and September. In the middle section during these 

months, both the actual weighted usable-habitat area and the 

simulated maximum weighted usable-habitat area are associated with this flow range. Weighted usable-habitat area in the 

lower management section is highest at flows lower than the 

75-percent exceedance flow for July, August, and September. 

In the lower section during these three months, some weighted 

usable-habitat area is available, but the normal range of flows 

does not include the simulated maximum weighted usablehabitat area.

A time-series habitat analysis associated with the historic 

streamflow, zero water withdrawals, and doubled water withdrawals was completed. During simulated historic drought 

periods, time-series habitat analysis shows weighted usablehabitat area to be limited for fast-generalist and pool-cover 

Physical Habitat Classification and Instream

Flow Modeling to Determine Habitat Availability

During Low-Flow Periods, North Fork

Shenandoah River, Virginia

By Jennifer L. Krstolic, Donald C. Hayes, and Peter H. Ruhl
2 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

guilds in the upper management section, for fast-generalist 

and pool-run guilds in the middle section, and for the poolcover guild in the lower section. The zero water-withdrawal 

scenario during historic low-flow periods shows improvement in weighted usable-habitat area for fast-generalist guild 

species in the upper management section and for pool-cover 

guild species in the lower section. The double water-withdrawal scenario simulation shows a total loss of fast-generalist 

guild weighted usable-habitat area during historic low-flow 

periods in the upper management section and a small decline 

in pool-cover guild weighted usable-habitat area in the lower 

management section. Simulated weighted usable-habitat areas 

are close to the maximum weighted usable-habitat area during 

a normal or wet historic summer period.

Streamflows that provide habitat at levels similar to those 

provided by the normal flow range (between the 25- and 75-

percent exceedance flows) were identified for each management section of the North Fork Shenandoah River. With the 

current flow regime, the model results indicate that weighted 

usable-habitat area does not become highly limited for fish 

until streamflows reach or fall below the 90-percent exceedance flows for multiple days in July, August, and September. 

During low-flow periods, weighted usable-habitat area is 

limited in the upper section, in particular. Water conservation 

measures and reduced withdrawals may help maintain flows 

that sustain habitat in the upper section and throughout the 

river during low-flow periods.

Introduction

The Shenandoah River basin in northwestern Virginia is 

an unregulated, rural basin with a growing population (30-percent growth 1980-2000) (Krstolic and Hayes, 2004) (fig. 1). 

Increasing development and increasing water withdrawals 

for public, industrial, and agricultural water supply threaten 

to reduce streamflows in the basin. Water-resources managers need more information to balance human water-supply 

needs with the daily streamflows necessary for maintaining 

the aquatic ecosystems of the basin. Prior to 1990, there was 

a scarcity of science-based information related to waterresources management in the Shenandoah basin. Since that 

time, groups from ten counties, incorporated cities, and towns 

in the Shenandoah River basin of Virginia and West Virginia 

(fig. 1) have begun working toward basinwide management of 

water resources. To meet the need for comprehensive information on hydrology, water supply, and instream-flow requirements of the Shenandoah River basin, the U.S. Geological 

Survey (USGS) and the Northern Shenandoah Valley Regional 

Commission (NSVRC) began a cooperative investigation of 

habitat availability during low-flow periods on the North Fork 

Shenandoah River in 1998. The overall study was enhanced 

through partnering with Virginia Polytechnic Institute and 

State University (VPI) in data collection and analysis. 

Zappia and Hayes (1998) related water availability 

to the physical habitat needs of fish and recreational uses 

in the Shenandoah River using Instream Flow Incremental 

Methodology (IFIM) techniques. Their study incorporated 

hydraulic information and literature-based fish habitat-suitability criteria to demonstrate the utility of scientific information for basinwide water-supply planning. Following Zappia 

and Hayes (1998) study on the main stem Shenandoah River, 

IFIM techniques were selected as the approach for the present 

study to investigate water availability and habitat on the North 

Fork Shenandoah River. There are two major tributaries to 

the Shenandoah River, however; the North Fork Shenandoah 

River was selected for study over the South Fork Shenandoah 

River because it has a growing population (67,551, 2000 U.S. 

Census) and the river discharge is less than that of the South 

Fork Shenandoah River, making water availability of greater 

concern.

The purpose of the present study is to enhance understanding of low-flow conditions, to relate water availability 

to physical habitat needs of fish, and to relate fish habitat to 

instream flows. It should be noted, however, that this study 

addresses fish habitat availability; habitat availability of other 

organisms was not investigated. The present study will provide 

scientific data to water-resources managers to assist them with 

setting target streamflows and selecting water-conservation 

goals. The methods and approach in this study can be applied 

to other basins in similar hydrogeologic settings.

The IFIM process usually includes the application and 

calibration of models such as the Physical Habitat Simulation Model (PHABSIM) (U.S. Geological Survey Fort Collins 

Science Center, 2001) or River Habitat Simulation Model 

(RHABSIM) (Thomas R. Payne and Associates, 1998), which 

are used to analyze hydraulic data along with the physical 

habitat requirements of aquatic organisms, or requirements of 

other instream and off-stream uses. The model output represents the habitat available for a selected set of streamflows. 

Inputs to the PHABSIM and RHABSIM models include 

physical habitat data, micro-scale fish habitat-suitability criteria (HSC), hydraulic data, and stage-discharge ratings. Coarse 

physical habitat data is gathered along rivers or reaches of 

interest using mesohabitat mapping techniques. Mesohabitat 

data is as part of the process of determining the potential fish 

species composition, abundance, and size or age structure that 

the river can support (Simonson and others, 1993; Armstrong 

and Richards, 2001; Armstrong and others, 2003; Parsiewics 

and others, 2004; Sutton and Morris, 2004). Channel and 

riparian conditions within and upstream from a reach can have 

a profound effect on the habitat present (Vannote and others, 

1980). Therefore, to accurately represent mesohabitat percentages for the reaches in the present study, the entire North Fork 

Shenandoah River was classified. 

Prior to the start of present study, a detailed assessment of 

the fish community of the North Fork Shenandoah River had 

not been published. Data on fish species abundance and microhabitat preferences were necessary to model habitat availability representative of the fish species in the North Fork Shenan-
Introduction 3

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Figure 1. Location of the North Fork Shenandoah River Basin, Virginia (study area).
4 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

doah River. The VPI Department of Fisheries and Wildlife 

conducted a fish community assessment, and documented the 

physical microhabitats used by each species (Persinger, 2003) 

for the NSVRC. The community assessment also included the 

development of fish HSC to be used by the USGS in the IFIM 

modeling process. 

Hydraulic data collection techniques provide habitat-specific stage and discharge relations needed for the IFIM modeling process. Measurements of depths, velocities, and watersurface elevations are typically used to establish ratings for a 

variety of habitat types. For the present study, hydraulic data 

were collected over a range of discharges by the USGS with 

the assistance of VPI. Hydraulic data were input to the RHABSIM model, a 1-dimensional water-surface profile model that 

uses stage-discharge ratings to simulate habitat conditions over 

a range of discharges. Because of the breadth of fish habitat 

conditions studied and the wide range of discharges modeled, 

the model results represent habitat and streamflow conditions that affect a large number of species on the North Fork 

Shenandoah River. 

RHABSIM modeling results provide comprehensive 

information about low-flow physical habitat conditions based 

on the current, historic, and simulated future flow regimes. 

As flows are reduced water quality conditions can become 

a greater factor than the availability of habitat. To address 

this issue, a companion study was completed in July 1999 

when the mean monthly streamflow was the lowest recorded 

since record-keeping began in 1925. Water-quality conditions 

documented in Krstolic and Hayes (2004) represent summer 

extreme low-flow conditions for the North Fork Shenandoah 

River. Krstolic and Hayes (2004) showed that most of the 

dissolved-oxygen concentrations at sites located in the upper 

reaches of the river were equal to or less than the State of 

Virginia’s water-quality minimum, and most of the pH values 

at sites in the downstream portion of the river were greater 

than the state water-quality maximum. Water temperatures 

for one site in the lower portion of the river exceeded the state 

water-quality maximum. The present study examines habitat 

availability during low-flow periods to add to the understanding gained through water quality research presented in Krstolic 

and Hayes (2004). 

The frequency of low-flow periods and increasing 

demands for water may affect instream flows and water-quality conditions throughout the North Fork Shenandoah River 

basin in the future. The model output, if used in conjunction 

with a socioeconomic analysis of water use and conservation, 

could be used by water-resources managers to make decisions 

about water-resources allocations that consider the habitat 

needs of fish and the water-use needs of humans. Similar 

studies that integrate habitat, instream flows, and water use 

are being incorporated into long-range water-resources plans 

in other basins in Virginia (Vadas and Weigmann, 1993). 

RHABSIM fish habitat results in combination with waterquality study results, current and projected water-use data, and 

projections about population growth could be helpful to waterresources managers in development of a plan to protect natural 

streamflow conditions, while meeting human water-supply 

needs within the North Fork Shenandoah River basin. 

Purpose and Scope

This report describes a classification of the mesohabitat 

of the North Fork Shenandoah River and documents the methods and findings of the habitat assessment and IFIM modeling 

process. The IFIM modeling process includes a synthesis of 

historic streamflow data, river hydraulics data, fish community 

structure data, fish habitat-suitability criteria, and recreationaluse suitability criteria. The objectives of this investigation are 

to enhance understanding of summer low-flow conditions in 

the North Fork Shenandoah River, relate water availability 

to physical habitat needs of fish, and develop a relation for 

the availability of suitable fish habitat and instream flows. 

Selected withdrawal scenarios are simulated, including the 

effect that zero water withdrawals and double water withdrawals have on fish habitat.

Hydrogeology

The study area encompasses the main stem North Fork 

Shenandoah River from the headwaters near the Virginia border with West Virginia to the confluence with the South Fork 

Shenandoah River (fig. 1). The North Fork Shenandoah River 

has a drainage area of 1,033 mi2. The North Fork Shenandoah 

River basin was divided into upper (miles 0–39.3), middle 

(miles 39.3–57.2), and lower (miles 57.2–107.3) sections for 

reporting study results (fig. 2). Streamflow-gaging stations are 

near the downstream end of each section: North Fork Shenandoah River at Cootes Store Va. (01632000), hereafter referred 

to as “Cootes Store”; North Fork Shenandoah River at Mount 

Jackson, Va. (01633000), hereafter referred to as “Mount Jackson”; and North Fork Shenandoah River near Strasburg, Va. 

(01634000), hereafter referred to as “Strasburg” (fig. 2). The 

drainage areas of these sections represent three hydrologically 

and geologically different areas within the basin, and are similar to basin divisions described by Hack and Young (1959). 

The headwater streams that feed the North Fork Shenandoah River originate in West Virginia, but the main stem 

begins in Rockingham County, Va., and flows through Shenandoah and Warren Counties in Virginia (fig. 1). From the 

headwaters, the river flows east until Timberville, Va., where it 

turns and flows northeast parallel to Interstate 81 and Highway 

11 to Strasburg, Va., and then turns east parallel to the Interstate 66 corridor to Front Royal, Va.

The North Fork Shenandoah River lies within the Valley and Ridge Physiographic Province. Basin topography is 

characterized by rolling hills and valleys, and is bordered on 

the eastern edge by Massanutten Mountain Range, which 

separates the North Fork Shenandoah River from the South 

Fork Shenandoah River (Virginia Department of Conservation 

and Economic Development, 1968) (fig. 1). The northeastsouthwest trending ridges of the Valley and Ridge Physio-
Introduction 5

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Figure 2. Upper, middle, and lower management sections, location of study reaches, and topography in the North Fork Shenandoah River Basin, Virginia.
6 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

graphic Province are formed by resistant quartzite, sandstone, 

and conglomerates; the valleys are underlain by more readily 

weathered limestone, shale, and dolomite (Hack, 1965; Hayes, 

1991). In the upper section, the North Fork Shenandoah 

River crosses the valleys and ridges on the west side of the 

basin, within mostly sandstone formations (Hack and Young, 

1959). The river flows along the eastern side of the valley 

floor near Massanutten Mountain in wide, gradual meanders 

until it reaches Edinburg, Va. The upper and middle sections include karst topography within limestone and dolomite 

formations. The karst features include caves, sinkholes, and 

springs. Downstream of Edinburg, Va., the river enters the 

lower section and Seven Bends area where it is characterized 

by extremely narrow meanders, with 180-degree reversals, 

as it winds in and out of the ridges on the eastern side of the 

valley (Hack and Young, 1959; Krstolic and Hayes, 2004). In 

this section, the river follows fracture zones in the Martinsburg 

Shale (Hack and Young, 1959; Hack, 1965), which helped to 

form the river morphology unique to the Seven Bends area. 

The river has cut down to the bedrock within the middle and 

lower reaches, giving it a shallow and wide channel (Krstolic 

and Hayes, 2004). 

Analysis of Historic Streamflow Data

Streamflows of the North Fork Shenandoah River basin 

have been monitored for more than 75 years. The long-term 

records from three streamflow-gaging stations (table 1) can 

be used to characterize the flow regime of the North Fork 

Shenandoah River. The station streamflow records represent 

slightly altered flow conditions owing to water withdrawals 

and return flows. Some of these withdrawals and returns are 

measured and documented and others are small, unregulated 

volumes that are not measured. The effect of water withdrawals on the North Fork Shenandoah River has not been 

assessed, but to this point (2004), streamflow records indicate 

that the river maintains a mostly natural flow regime. 

Flow-duration curves can be used to describe the distribution of past flows and indicate the potential magnitude and 

frequency of occurrence of streamflows under similar climatic, 

land-use, and water-use conditions. A flow-duration curve is 

a cumulative frequency curve that shows the percentage of 

time specified discharges were equaled or exceeded during 

a given period, and combines the flow characteristics of a 

stream throughout the range of discharge, without regard to 

the sequence of occurrence (Searcy, 1969). The curves can be 

based on flows for the entire year or for specific time frames 

such as individual months or seasons. 

Streamflows in the North Fork Shenandoah River fluctuate between flood-flow, normal-flow and low-flow conditions 

seasonally and yearly. Within the North Fork Shenandoah 

River basin, annual flow-duration curves representing the 

entire water year are used to calculate the daily mean flows 

equivalent to the 25- and 75-percent exceedance values (table 

2, fig. 3), which are referred to in this report as the normal 

range of flows. This range only represents 50 percent of the 

data collected, so within a natural flow regime, the flow is 

outside of this range 50 percent of the time. The exceedance 

flows describe common flow patterns based on data collected 

throughout the entire period of record, and provide a standard 

for comparison with individual years or months. For this study, 

months with high temperatures, little precipitation (Southeast 

Regional Climate Center, 2003), low streamflow, and high 

water-use demands are of particular interest. Flow-duration 

curves representing the combined historic data from July, 

August, and September were selected to characterize the ”lowflow period” exceedance flows for the North Fork Shenandoah 

basin (table 2). The 25- and 75-percent exceedance values 

for data from July, August, and September were used in this 

report to represent the normal range of flows for the low-flow 

period. Years having flows much lower than the normal range 

of flows for July, August, and September may be classified as 

dry years. 

Table 1. Continuous monitoring streamflow-gaging stations on the North Fork Shenandoah River, Virginia.

[mi2, square miles]

Station 

number Station name Drainagearea (mi2) Operating agency Period of record

01632000 North Fork Shenandoah River at 

Cootes Store, Va. (Cootes Store) 210 U.S. Geological Survey 1925–present

01633000 North Fork Shenandoah River at

Mount Jackson, Va. (Mount Jackson) 506 Virginia Department of Environmental Quality 1943–present

01634000 North Fork Shenandoah River near

Strasburg, Va. (Strasburg) 768 U.S. Geological Survey 1925–present
Analysis of Historic Streamflow Data 7

Table 2. Monthly, seasonal, and annual exceedance flows for three streamflowgaging stations on the North Fork Shenandoah River, Virginia.—Continued

[ft3/s, cubic feet per second; Q.90–Q.25 =, value representing the 90-, 75-, 50-, or 25-percent exceedance value for the monthly, seasonal, or annual flows as noted; Values in bold type

represent normal range of flows for the low-flow period]

Time period Exceedance 

value

Cootes Store1

01632000

Mount Jackson2

01633000

Strasburg1

01634000

Discharge, in 

ft3/s

Discharge, in 

ft3/s

Discharge, in 

ft3/s

October Q.90 = 2.3 32 88

Q.75 = 4.5 45 113

Q.50 = 12 74 156

Q.25 = 50 153 267

November Q.90 = 4.6 40 104

Q.75 = 10 58 132

Q.50 = 30 100 185

Q.25 = 97 233 380

December Q.90 = 7 47 113

Q.75 = 27 77 161

Q.50 = 73 184 305

Q.25 = 168 383 561

January Q.90 = 15 58 140

Q.75 = 41 122 210

Q.50 = 100 266 410

Q.25 = 230 457 10,276

February Q.90 = 27 89 164

Q.75 = 66 194 315

Q.50 = 147 360 565

Q.25 = 299 640 946

March Q.90 = 67 188 301

Q.75 = 114 288 434

Q.50 = 208 495 700

Q.25 = 400 870 1,270

April Q.90 = 59 156 288

Q.75 = 89 234 394

Q.50 = 167 383 604

Q.25 = 348 706 1,090

May Q.90 = 36 127 224

Q.75 = 60 187 313

Q.50 = 121 318 502

Q.25 = 265 550 840

June Q.90 = 14 68 150

Q.75 = 23 109 206

Q.50 = 44 169 300

Q.25 = 99 279 471

July Q.90 = 4 39 100

Q.75 = 8.5 61 136

Q.50 = 18 94 193
8 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Table 2. Monthly, seasonal, and annual exceedance flows for three streamflowgaging stations on the North Fork Shenandoah River, Virginia.—Continued

[ft3/s, cubic feet per second; Q.90–Q.25 =, value representing the 90-, 75-, 50-, or 25-percent exceedance value for the monthly, seasonal, or annual flows as noted; Values in bold type

represent normal range of flows for the low-flow period]

Time period Exceedance 

value

Cootes Store1

01632000

Mount Jackson2

01633000

Strasburg1

01634000

Discharge, in 

ft3/s

Discharge, in 

ft3/s

Discharge, in 

ft3/s

Q.25 = 41 158 292

August Q.90 = 1.4 26 84

Q.75 = 3.5 44 115

Q.50 = 13 74 169

Q.25 = 46 169 300

September Q.90 = 1.3 28 83

Q.75 = 2.7 41 108

Q.50 = 9.8 64 149

Q.25 = 32 139 254

Annual Q.90 = 4.6 43 110

Q.75 = 15 76 160

Q.50 = 61 182 310

Q.25 = 178 418 630

July Aug Sept3 Q.90 = 1.6 30 87

Q.75 = 4.4 47 119

Q.50 = 14 78 171

Q.25 = 40 155 283

Spring4 Q.90 = 48 147 260

Q.75 = 86 230 373

Q.50 = 164 388 590

Q.25 = 338 710 1,060

Summer5 Q.90 = 3 36 99

Q.75 = 9 62 143

Q.50 = 23 112 214

Q.25 = 64 207 367

Fall6 Q.90 = 2.1 32 90

Q.75 = 5 47 118

Q.50 = 15 78 163

Q.25 = 58 172 296

Winter7 Q.90 = 14 58 130

Q.75 = 40 119 210

Q.50 = 101 268 416

Q.25 = 231 520 758

 1Historical data range 1925–2002.

 2Historical data range 1944–2002.

 3Reference low-flow months, July, August, and September.

 4Spring months include March, April, and May.

 5Summer months include June, July, and August.

 6Fall months include September, October, and November.

 7Winter months include December, January, and February.
Analysis of Historic Streamflow Data 9

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Figure 3. Annual and seasonal flow-duration curves for three 

streamflow-gaging stations on the North Fork Shenandoah River, 

Virginia: at Cootes Store, Va. (01632000) (A); at Mount Jackson, Va. 

(01633000) (B); near Strasburg, Va. (01634000) (C).
10 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

The frequency and duration of low flows are important 

descriptors of low-flow conditions. Assessments of such 

hydrologic indices are important for understanding and 

predicting the effects of altered flow regimes on stream biota 

(Olden and Poff, 2003). The flow regime for the North Fork 

Shenandoah River can be further defined by examining the 

duration of the July, August, and September 25-, 50-, 75-, 90-, 

and 99- percent exceedance flows (table 3). By definition, 

90-percent exceedance flows (whether annual, monthly, or 

seasonal) occur 10 percent of the time. In past dry years on the 

North Fork Shenandoah River, flows equal to or less than the 

90-percent exceedance flow for July, August, and September 

occurred more than 50 percent of the time during low-flow 

months (table 4). 

On average, daily values equal to or less than the 90-

percent exceedance flows for July, August, and September 

for the Cootes Store, Mount Jackson, and Strasburg streamflow-gaging stations were recorded 1-4 days per month based 

upon the historic record for each station. During normal to 

wet years, these 90-percent exceedance flows are rare during 

July, August, and September, but during dry years or seasons, 

most daily mean flows are equal to or less than these values. 

Throughout the historic period, when daily mean flows equal 

to or less than the 90-percent exceedance flows for July, 

August, and September occur at least 50 percent of the time 

during some summer and fall months, it is likely that instream 

flows were limited (figures 4, 5, 6). This flow pattern occurred 

in the North Fork Shenandoah River basin in 1930, 1964–

1966, 1999, and 2002. Many summer and fall months during 

these years had daily mean flows lower than the 90-percent 

exceedance flows for July, August, and September for 15 or 

more days per month (table 4). Although the analysis does 

not take into account whether the days below the exceedance 

flow were consecutive, it is likely that these low-flow days 

were consecutive because they occurred more than 15 days 

per month. Based on the historic streamflow data, dry periods 

meeting the above criteria occurred on approximately a 10- to 

30-year cycle (figs. 3, 4, 5).

Aquatic biota have different seasonal flow needs related 

to the magnitude, frequency, and duration of flows (Poff and 

others, 1997; Richter and others, 1997, Richter and others, 

2003). The normal range of flows for each season overlap, but 

the normal range of flows for winter and spring are substantially higher than the normal range of flows for summer and 

fall for the North Fork Shenandoah River (table 2). Low-flow 

statistics developed from the summer and fall months are not 

equivalent to those developed from winter and spring months. 

A streamflow that represents a low flow during one season can 

be a high flow during another. For example, a low flow of 48 

ft3/s at the Cootes Store station (table 2) would be expected 

infrequently during spring, but would be expected frequently 

during fall, and is within the high end of the normal range of 

flows for fall. Likewise, annual flow statistics do not adequately represent seasonal or monthly conditions. Streamflow 

statistics that describe the natural variations in flows for different seasons of the year are needed to fully describe natural 

flow regimes in an effort to understand how they affect the fish 

community.

Table 3. Average and maximum number of days in July, 

August, and September that streamflows were equal to or less 

than specified low-flow period exceedance values on the North 

Fork Shenandoah River, Virginia.

[avg, average number of days at the given exceedance flow; max, maximum 

number of days at the given exceedance flow]

 Upper management section

Cootes Store1

01632000 

July August September 

Exceedance

value avg max avg max avg max

25 23.6 31 23.3 31 23.9 30

50 9.9 31 14.5 31 15.7 30

75 2.7 31 8.0 31 9.3 30

90 1.0 25 3.5 31 4.2 30

99 0.0 0 0.5 11 0.3 12

Middle management section

Mount Jackson2

01633000 

July August September 

Exceedance

value avg max avg max avg max

25 22.4 31 22.1 31 22.7 30

50 11.0 31 14.5 31 15.9 30

75 3.7 31 7.3 31 8.0 30

90 1.5 31 3.7 27 3.1 22

99 0.4 31 0.5 17 0.3 14

Lower management section

Strasburg1

01634000

July August September 

Exceedance

value avg max avg max avg max

25 22.4 31 22.7 31 23.4 30

50 11.4 31 14.1 31 16.3 30

75 4.2 31 7.1 31 8.4 30

90 1.9 31 3.2 30 3.4 27

99 0.4 22 0.4 22 0.3 10

1 Historical data range 1925–2002.

 2 Historical data range 1943–2002.
Analysis of Historic Streamflow Data 11 ��

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Figure 4. Number of days per summer month (July, August, September, and October) for the years 1995–2002 with streamflow values equal to or less than the 90-percent exceedance flow (1.6 cubic feet per second) for the Cootes Store streamflow-gaging station (01632000) on the North Fork Shenandoah River, Virginia.
12 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

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Figure 5. Number of days per summer month (July, August, September, and October) for the years 1943–2002 with streamflow values less than the 90-percent exceedance flow (30 cubic feet per second) for the Mount Jackson streamflow-gaging station (0163300) on the North Fork Shenandoah River, Virginia.
Analysis of Historic Streamflow Data 13 ��

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Figure 6. Number of days per summer month (July, August, September, and October) for the years 1925–2002 with streamflow values less than the 90-percent exceedance flow (87 cubic feet per second) for the Strasburg streamflow-gaging station (0163400) on the North Fork Shenandoah River, Virginia.
14 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Mesohabitat Classification 

Mesohabitats were classified and mapped to identify, 

describe, and quantify the mesohabitat types within the North 

Fork Shenandoah River. In this report, the term mesohabitat 

refers to a moderately large hydrogeomorphic habitat within 

a stream, such as a riffle, run, or pool, that has a relatively 

homogeneous channel shape and hydraulic characteristics and 

that behaves as a unit in response to changes in flow (Vadas, 

1992; Vadas and Orth, 1998). Habitat data are collected 

primarily to document the relative quantity and quality of 

habitat availability for fish within a river (Simonson and others, 1993). Sharp changes in depth and (or) surface turbulence 

often delineate mesohabitat types (Vadas and Orth, 1998). 

The inventory of mesohabitats along the main stem of the 

North Fork Shenandoah River allowed for detailed hydrologic 

and fish community data collection to be prioritized within 

river reaches containing the predominant mesohabitat types, 

and assisted with weighting RHABSIM model transects to 

adequately simulate mesohabitat types in the river. 

Methods 

Mesohabitat mapping was conducted during low-flow 

periods between September 1998 and November 2002. During 

the data-collection period, flows ranged from 1.7 to 40 ft3/s at 

Cootes Store, from 29 to 173 ft3/s at Mount Jackson, and from 

108 to 377 ft3/s near Strasburg. Streamflow values during data 

collection ranged from the 50- to 95-percent annual exceedance values. 

Mesohabitat mapping was conducted by canoe or on foot 

for the length of the North Fork Shenandoah River. As each 

change in mesohabitat type was encountered, the boundary 

location was recorded using a global positioning system (GPS) 

receiver. The mesohabitat type was noted, and mesohabitat 

length, average and maximum water depth, channel width, and 

bed substrate were measured or estimated visually. Mesohabitat length was estimated in the field (using the canoe as a scale 

reference) for mesohabitat less than 50 ft long, or measured 

with an infrared rangefinder (accuracy plus or minus 3 ft) or 

by using GPS-collected start and end points. As the canoe was 

paddled slowly through a habitat unit, water depth was measured with a surveyor’s rod and channel width was measured 

with the infrared rangefinder. The predominant substrate type 

and particle size were estimated visually. 

Mesohabitat was classified into three general categoriesriffles, runs, and pools- which were further divided into two or 

more subcategories (Table 5). These categories are hierarchical 

and were developed based on lateral and hydraulic (depthturbulence) characteristics that were visually assessed (after 

Vadas and Orth, 1998). Qualitative observations of water-surface gradient, water velocity, bed substrate type and size, and 

channel morphology were combined with depth measurements 

to classify each mesohabitat unit. 

Table 4. The number of days flows were equal to or less

than the 90-percent exceedance value for July, August, and 

September during dry years on the North Fork Shenandoah 

River, Virginia.

[n.d., no data, station was not in service during the year]

Year July Aug Sept 3-month 

average

Percent of 

days

Cootes Store

1930 6 31 30 22 72.0

1964 12 30 23 22 69.9

1965 5 29 30 21 68.8

1966 11 29 13 18 57.0

1999 25 18 0 14 46.2

2002 0 4 17 7 22.6

Mount Jackson

1930 n. d. n. d. n. d. n. d. n. d.

1964 3 27 22 17 55.9

1965 1 15 10 9 28.0

1966 18 23 13 18 58.1

1999 31 19 3 18 57.0

2002 4 27 21 17 55.9

Strasburg

1930 15 26 23 21 68.8

1964 4 25 17 15 49.5

1965 3 1 1 2 5.4

1966 21 23 13 19 61.3

1999 31 22 0 18 57.0

2002 4 8 18 10 32.3

Habitat Classification 

Habitat classification on the North Fork Shenandoah 

River included data collection at three scales. Physical 

mesohabitat information at the scale of one river width was 

collected with mapping techniques in order to document variations in habitat from the headwaters to the mouth of the river. 

Site-specific transect data were collected at low, medium, and 

high flows to document variations of habitat with streamflow. 

Species-specific microhabitat use observations were made to 

document the instream conditions preferred by fish species on 

the North Fork Shenandoah River. When used together within 

the RHABSIM habitat modeling program, these data help in 

the determination of flows which provide suitable habitat for 

the fish of the North Fork Shenandoah River.
Habitat Classification 15

Table 5. Habitat type descriptions used for classification of mesohabitat on the North Fork Shenandoah River, 

Virginia.

Habitat

type Description

Riffle Shallow rapids, with fast velocities, in an open stream where a turbulent water surface is created by 

obstructions that are wholly or partly submerged. Water depth is generally less than 1 foot deep.

Bedrock riffle Formed by shallow water running over bedrock.

Particle riffle Formed by a deposit of discrete particles such as boulders, small rocks (cobbles), gravel, and sand. 

Particle riffles are usually associated with islands or large channel bars.

Run Swift moving areas characterized by predominantly smooth to slightly turbulent flow. The water surface is usually flat and is not broken by the substrate. Water depth is typically 1–4 feet deep.

Particle run Formed by a gently sloping bed with a fairly consistent and uniform depth. Substrate is thin to thick 

deposits of cobbles, pebbles, gravel, and/or sand.

Bedrock run Formed by a gently sloping bed with a fairly consistent and uniform depth. Substrate is bedrock with 

little silt or sand.

Pocket run Characterized by shallow areas of bedrock interspersed with a mosaic of deeper holes or “pockets” 

that provide cover for fish. The pockets are more than 4 feet deep and generally 10–30 feet across. 

Pocket runs are distinguished from other runs in that they lack consistent and uniform depth. Pockets are encountered every 20 to 100 linear feet and found across the entire stream channel.

Pool Areas with reduced or barely perceptible surface velocity, with a smooth, unbroken water surface. 

Water depth is greater than 4 feet deep.

Natural pool Formed by a naturally occurring channel obstruction such as a bedrock control, island, large gravel 

bar, or a meander bend.

Artificial pool Formed by an artificial channel obstruction such as a dam.

Backwater Occurs along the edge of the channel. Backwaters are shallow pools that often occur on the downstream side of a large gravel bar or to one side of a mid-channel bar where water no longer flows 

around the bar. 
16 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

The GPS-collected latitude and longitude coordinates 

were entered into a geographic information system (GIS) 

to create a GIS layer of mesohabitat boundary points. Short 

mesohabitat units (3-10 ft long) usually lacked GPS locations 

defining the beginning or end of the unit. Field notes were 

used to indicate where points should be added to complete 

the habitat boundary-point dataset. Points were added around 

meander bends and others were moved to mid channel to 

increase the accuracy of the length calculations. The adjusted 

GIS point layer was used to create a GIS line layer with accurate mesohabitat unit lengths and tabular information representing other measured parameters.

Results 

Mesohabitat characteristics are reported for the upper, 

middle, and lower management sections of the North Fork 

Shenandoah River basin. For each mesohabitat type, the number of mesohabitat units, total length, percentage of the river 

length within the management section, and percent of the total 

river length are reported (table 6). 

The habitat of the North Fork Shenandoah River is 

composed of 14.0 percent riffles, 67.3 percent runs, and 18.7 

percent pools. Particle riffles are the most numerous riffle 

mesohabitat with 500 identified, followed by 155 bedrock 

riffles (table 6). The average length of particle and bedrock riffles is 114 ft and 143 ft respectively, but short riffles of about 3 

ft in length are common. Most of the particle riffles are located 

along islands or narrow bends in the river. Particle runs are 

the most numerous run mesohabitat with 508 identified, followed by 256 bedrock runs, and 52 pocket runs (table 6). Most 

individual runs are greater than 300 ft in length, with average 

lengths of 344 ft, 765 ft, and 183 ft for particle, bedrock, and 

pocket runs, respectively. Natural pools are the most numerous 

pool mesohabitat with 102 identified, followed by 18 artificial 

pools, and 41 backwater areas (table 6). Where pools are present, they cover extensive sections of river, with average lengths 

of 559 ft, 2,083 ft, and 270 ft for natural pools, artificial pools, 

and backwater areas. Most artificial pools on the North Fork 

Shenandoah River are formed behind abandoned low bridges, 

and broken, small, low-head dams previously used to divert 

water to mill races for saw mills and grist mills during the late 

1800’s and early 1900’s (Trout, 1997).

Substrate type and habitat-unit length differentiate the 

form and function of habitat between the upper, middle, and 

lower sections of the North Fork Shenandoah River. The upper 

section contains short mesohabitat units, with many repeating riffle, run, riffle sequences. Particle-substrate riffles and 

runs are most common. The source of the particle substrate is 

the siliceous rock from the headwater area that is transported 

great distances downstream from the source (Hack and Young, 

1959). Although the river itself is flowing through a shale 

valley, the bedrock is soft relative to the sandstone coarse 

particulate substrate introduced from the tributaries. The shale 

bedrock is more easily eroded and broken up into small fragments that are carried away, resulting in a smaller percentage 

of shale particulate substrate on top of the bed relative to the 

sandstone substrate (Hack and Young, 1959). 

The North Fork Shenandoah River receives flow from 

Smith Creek, Narrow Passage Creek, and Stony Creek in the 

middle section. Stony Creek marks the downstream end of 

the Seven Bends area, as the river transitions from the short, 

shallow mesohabitat units of the upper section into the longer 

mesohabitat units of the lower section. The upper and middle 

sections are covered primarily by cobbles and boulders. The 

middle management section is roughly half the total length 

of the upper section; however, the number of riffle habitat 

units (103) is one-fourth that of the upper section (406). The 

average length of an individual mesohabitat unit in the middle 

section is greater than the average length in the upper section, 

marking the transition between short, alternating sequences 

of riffles and runs to longer stretches of riffles and runs. Few 

pools or backwater mesohabitat units were identified in the 

middle section. 

 The lower section is the longest (50 mi), and contains 

long bedrock runs which frequently lead into artificial pools. 

In the meandering reaches of the lower section, the bed is 

mostly exposed bedrock (Hack and Young, 1959). There is 

less sandstone and other particle substrate on the bed in this 

section than in the upper or middle sections, which suggests that in the meandering reaches, greater energy has 

been expended in the excavation of rock by elongation of the 

channel than by the transportation of rock fragments (Hack 

and Young, 1959). The lower section of the North Fork 

Shenandoah River has seven artificial pools, which make up 

the longest individual mesohabitat units in this section and in 

the river (average 4,175 ft). The bedrock runs in this section 

are the second-longest individual mesohabitat units in the river 

(average 1,076 ft) and often lead up to the artificial pools.

Differences in the abundance and distribution of mesohabitat types from upstream to downstream can be seen by 

examining a plot of cumulative distribution of mesohabitat 

lengths (fig. 7). Particle riffles are more abundant than bedrock 

riffles throughout the river and especially within the upper and 

middle sections. Bedrock riffle mesohabitats are not abundant 

in the upper section, but increase in abundance in the middle 

and lower sections. Particle runs make up the greatest length 

of mesohabitat in the upper and middle sections, but are surpassed in length by bedrock runs in the lower section (fig. 7). 

The middle section is a transitional section between predominantly particle substrate in the upper section and bedrock 

substrate in the lower section. Natural pool mesohabitats are 

almost equally abundant in the upper, middle, and lower sections. Artificial pools have an irregular pattern of occurrence 

related to the presence of small dams along the river. 
Habitat Classification 17

Table 6. Results of the mesohabitat classification and mapping for three management sections of the North Fork Shenandoah River, Virginia.

Habitat type

Upper section Middle section Lower section Entire river

Number 

of units

Unit 

average 

length 

(feet)

Total 

length 

(miles)

Percentage 

of section

Number 

of units

Unit 

average 

length 

(feet)

Total 

length 

(miles)

Percentage 

of section

Number 

of units

Unit 

average 

length 

(feet)

Total 

length 

(miles)

Percentage 

of section

Number 

of units

Unit 

average 

length 

(feet)

Total 

length 

(miles)

Percentage 

of entire 

river

Particle riffle 354 96.9 6.5

18.5

71 111.5 1.5

12.3

75 197.1 2.8

11.1

500 114.0 10.8

14.0

Bedrock riffle 52 71.1 0.7 32 115.5 0.7 71 208.2 2.8 155 143.1 4.2Particle run 356 280.3 18.9

64.0

81 417.2 6.4

69.5

71 587.5 7.9

69.1

508 344.0 33.1

67.3 Bedrock run 84 289.1 4.6 41 746.9 5.8 131 1,076.2 26.7 256 765.2 37.1

Pocket run 17 496.9 1.6 9 29.3 .05 26 20.3 0.1 52 182.8 1.8Natural pool 59 429.6 4.8

17.5

25 443.5 2.1

18.2

18 1,144.0 3.9

19.8

102 559.1 10.8

18.7 Artificial pool 7 678.9 .9 4 924.0 .7 7 4,148.6 5.5 18 2,082.7 7.1

Backwater 25 253.4 1.2 8 264.0 .4 8 330.0 .5 41 270.4 2.1Totals 954 207,5041 39.3 100.0 271 92,9281 17.6 100.0 407 264,5281 50.1 100.0 1,632 564,9601 107.0 100.0

1Total length in feet within the section.
18 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

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Figure 7. Cumulative length of riffle (A), run (B), and pool (C) mesohabitat types in the upper, middle, and 

lower management sections of the North Fork Shenandoah River, Virginia. River mile zero represents the 

confluence of smaller tributaries to form the headwaters of the North Fork Shenandoah River.
Habitat Classification 19

Hydraulic Data Collection in the Predominant 

Mesohabitat Types

Hydraulic data were used during model calibration and 

simulation to develop relations between water-surface elevation and discharge, and between water velocity and discharge. 

Data were collected on the North Fork Shenandoah River 

between April 1999 and November 2002. 

Selection of Reaches 

Six river reaches were selected for collection of hydraulic data on the North Fork Shenandoah River between Cootes Store, Va., and the confluence with Passage Creek. The 

reaches are referred to by place names of nearby features, and 

listed in order from upstream to downstream: Plains Mill, Laurel Hill Farms, Spring Hollow, Posey Hollow, Route 648, and 

Winchester Dam (fig. 2 and table 7). The predominant mesohabitat types in the river are represented in the reaches. The 

original scope of the project focused on the Seven Bends area 

of the North Fork Shenandoah River; therefore, five of the six 

reaches are in the northern end of the basin, in the middle and 

lower sections of the river. As the study progressed, the Plains 

Mill reach near Cootes Store, Va. was added to incorporate the 

upper section of the North Fork Shenandoah River (fig. 2). 

Description of Reaches and Transects 

Study reaches varied in length from 150 ft to 2000 ft, and 

in width from 100 ft to 200 ft. All reaches contained one or 

more mesohabitats, and three to eight semipermanent transects 

(following Bovee, 1997) (table 8). Transects were placed in 

sections of the river where the mesohabitat was homogeneous 

across the channel. Most reaches began with a downstream 

hydraulic control or riffle. The right bank and left bank were 

designated when looking downstream, with the right bank designated headpin and left bank designated tailpin in most cases. 

The ends of each transect were marked with rebar and labeled 

with numbered metal tags. Transects were extended out onto 

the floodplain to a level greater than bankfull. Verticals used 

in velocity, depth, and substrate measurements were spaced 

equally along each transect at constant intervals of either 3, 

4, or 5 ft based upon the width of the river (following Bovee, 

1997).

Standard PHABSIM data collection procedures (Bovee, 

1997) were used to collect channel and floodplain topographic 

information for the model. Horizontal and vertical surveys 

of benchmarks, transect headpin and tailpin elevations, and 

channel features were conducted with a surveying level or 

a total station. The surveys provided information such as 

distance between transects, water-surface slope, bed-elevation 

profiles, stage-zero-flow elevation, water depths, and benchmark locations and elevations. The benchmarks used for the 

transect headpin and tailpin elevation surveys also served as 

benchmarks for water-surface elevation (WSL) measurements 

during hydraulic data collection. 

Hydraulic Data Collection Methods 

Hydraulic measurements were made in riffles, runs, and 

pools with a variety of substrates and cover types between 

April 1999 and November 2002. Each reach was visited a minimum of three times during hydraulic data collection to measure WSL, water depths, water velocities, transect discharges, 

and a best-estimate reach discharge during low-, medium,- and 

high-flow conditions. Hydraulic data collection was completed 

during wadeable flows, so the measurements are most reliable 

for low to normal flows. Some of the best-estimate discharges 

measured during the hydraulic data collection were close in 

value, but the range of flows measured for each reach were 

wide enough to develop a stage-discharge rating for the modeled flows. The best-estimate discharges measured for each 

reach were used as calibration discharges for the modeling 

phase of this research (table 9). 

Table 7. Locations of river reaches studied during hydraulic data

collection on the North Fork Shenandoah River, Virginia.

[Location information for the partial record station at each study reach (White and 

others, 2002). Reaches are presented in upstream to downstream order; DMS, degrees 

minutes seconds; NAD27, North American datum of 1927.]

Reach name Station number Latitude

DMS (NAD27)

Longitude 

DMS (NAD27)

Plains Mill 01632530 38 38 56 W 78 42 25 N

Laurel Hill Farms 01633575 38 50 12 W 78 31 39 N

Spring Hollow 01633640 38 53 12 W 78 28 46 N

Posey Hollow 01633800 38 56 28 W 78 23 09 N

Route 648 01633820 38 57 15 W 78 23 03 N

Winchester Dam 01635210 38 58 52 W 78 17 25 N
20 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Table 9. Best-estimate calibration discharges for each hydraulic 

data-collection reach on the North Fork Shenandoah River, Virginia.

[Within each category (low, medium, and high) if more than one discharge is listed, 

data collection occured over multiple days. Transect data are represented by

different discharges; ft3/s, cubic feet per second]

Hydraulic Reach

Calibration discharge (ft3/s)

Low Medium High

Plains Mill 22.5 109, 121 264, 308, 379, 438

Laurel Hill Farms 93.8 120 400

Spring Hollow 94.4 126 432

Posey Hollow 122 219 666

Route 648 83.34, 86.98 136 444, 526

Winchester Dam 195, 218 654, 696 1,430

Table 8. Mesohabitat types represented by transects in the hydraulic data-collection reaches on 

the North Fork Shenandoah River, Virginia. 

[Transects are numbered in downstream to upstream order, beginning with number 1.]

Transect 

ID Habitat type Transect ID Habitat type Transect ID Habitat type

Laurel Hill Farms Spring Hollow Posey Hollow

5 Particle riffle 5 Particle riffle 5 Pocket run

4 Particle riffle 4 Particle riffle 4 Bedrock run

3 Particle run 3 Particle riffle 3 Bedrock run

2 Particle run 2 Particle riffle 2 Pocket run

1 Particle run 1 Particle run 1 Bedrock riffle

Plains Mill Route 648 Winchester Dam

7 Particle run 8 Bedrock run 3 Artificial pool

6 Particle run 7 Pocket run 2 Artificial pool

5 Particle run 6 Pocket run 1 Artificial pool

4 Natural pool 5 Bedrock run

3B Natural pool 4 Pocket run

3A Particle run 3 Pocket run

3 Particle riffle 2 Bedrock run

2 Natural pool 1 Bedrock riffle

1A Particle run
Habitat Classification 21

For each day of data collection, WSLs were measured 

along one bank at each transect headpin or tailpin before and 

after data collection. WSLs were determined with a surveying level to the nearest 0.001 ft from a designated benchmark. 

A tagline was stretched across a transect, and water depths 

and velocities were recorded at the specified verticals for the 

reach. Velocity measurements were made using Price AA 

and Pygmy meters (to the nearest 0.01 ft/sec), or an electromagnetic flow-meter (to the nearest 0.1 ft/sec) mounted 

on a top-setting wading rod or hand line. Depth and velocity measurements followed USGS procedures for discharge 

measurements (Buchanan and Somers, 1969), except that the 

spacing between velocity readings, or verticals, was constant. 

Depth and velocity measurements from one transect per reach 

were used to calculate the best-estimate reach discharge. For 

reaches that did not have a transect suitable for discharge measurements, a discharge measurement was made downstream of 

the reach. Although complete hydraulic data collection could 

not always be accomplished at all transects at a reach in a 

single day, WSLs were measured for all transects in the reach. 

Fish-Community Sampling and Microhabitat 

Observations

Typically, IFIM studies examine one or two species of 

importance and develop relations between the species habitat needs and discharge; these relations can then be used in 

the management of water levels in the stream. For the IFIM 

process to provide the most useful information on habitat for 

the North Fork Shenandoah River, which has a diverse fish 

community, all resident fish species and life stages need to be 

considered (Orth, 1987; Braaten and Berry, 1997; Persinger, 

2003). In an effort to represent all species, but not model each 

species individually, fish were grouped into guilds (Vadas and 

Orth, 2000) for development of HSC. A fish guild is a group 

of fish or life stages that use microhabitats in a similar way. 

The combined abundance of species in a guild can reflect 

changes in limiting factors (Austin and others, 1994). For 

example, the combined abundance of riffle guild fish may be 

low if a limiting factor, such as water depth, has been lower 

than suitable for an extended period of time. 

Community Sampling

Species composition and abundance on the North Fork 

Shenandoah River were described to document the fish and 

habitats utilized along the river. This portion of the study was 

conducted by VPI faculty, staff, and students from the Department of Fisheries and Wildlife during the summers of 2001 

and 2002. Fish sampling was conducted at seven locations 

on the North Fork Shenandoah River, of which five also were 

used as hydraulic data collection sites (Persinger, 2003). Fish 

were sampled primarily by use of throwable anode electrofishing and underwater observation done by snorkeling during 

wadeable flows.

Thirty-seven species were identified and grouped into 

four guilds (Persinger, 2003) (table 10). Fish species and life 

stages were classified as members of the riffle guild, fastgeneralist guild, pool-run guild, or pool-cover guild following 

guild structure adapted from Vadas and Orth (2000) (Persinger, 2003). The four guilds are organized along a continuum 

of habitat preference from fish preferring shallow depths with 

fast velocities, to deep depths with slow velocities. The riffle 

guild includes species of life stages that live in sections of the 

river with shallow depths and fast velocities. The fast-generalist guild includes species and life stages that live in sections 

with shallow to moderate depths and fast velocities. The fish 

in this group overlap in their velocity preferences with the 

riffle guild fish, and overlap in their depth preferences with the 

pool-run and pool-cover guilds. The pool-run guild includes 

species and life stages that prefer deeper depths with moderate velocities. The pool-cover guild includes species and life 

stages that prefer the lowest velocities and deepest depths, 

and generally utilize cover objects when present. Five species 

were considered members of more than one guild, depending 

upon the life stage of the fish (Persinger, 2003). For example, 

the spotfin shiner (Cyprinella spiloptera) was a member of 

the pool-cover guild during its juvenile and young-of-year life 

stages, but was a member of the fast-generalist guild as an 

adult (Persinger, 2003).

Microhabitat Observations 

The physical microhabitat parameters of water depth, 

water velocity, and substrate type were measured at each 

location where a fish was observed. These parameters were 

arithmetically combined to describe the physical habitat 

conditions used by species of various life stages in the river. 

Depth was measured with a wading rod (to the nearest 0.10 

ft). Water velocity was measured with an electromagnetic flow 

meter (to the nearest 0.10 ft/sec). Substrate within a 1-m2 area 

around each fish observation location was assessed by assigning a channel index value–a composite measure of dominant 

substrate, subdominant substrate, embeddedness, and all cover 

items. Individual channel indexes were computed based on 

each substrate evaluation using a modified Wentworth classification scheme (Trihey and Wegner, 1981; Platts and others, 

1983; Newcomb, 1992; Bovee, 1997). Substrate variables 

were recorded using a system of codes and quartiles and summarized as one number, the channel index (tables 11–13). For 

example, a location observed to have a dominant substrate of 

small cobble, subdominant substrate of large gravel, cover of 

a root wad and small-velocity shelter, and embeddedness of 

10 percent would be coded as 08; 07; 08, 02; 1. The suite of 

codes was simplified to a 3-part numerical code, or channel 

index, based on dominant substrate (table 11), cover presence 

(0.1) or absence (0.0) (table 12), and embeddedness (quartile 

1 = 0.01, quartile 2 = 0.02, quartile 3 = 0.03, quartile 4 = 0.04) 

(table 13). For the previous example, the computed channel 

index would be 8.11. 
22 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Table 10. Species and guild classification for fish identified in 

the North Fork Shenandoah River.

[Table modified from Persinger, 2003; J, juvenile; Y, young-of-year;

A, Adult] 

Species Scientific name

Riffle guild

Greenside darter Etheostoma blennioides 

Mottled sculpin Cottus bairdi

Central stoneroller Campostoma anomalum

Bluehead chub (J) Nocomis leptocephalus

River chub (Y) Nocomis micropogon

Longnose dace Rhinichthys cataractae 

Fast-generalist guild

Potomac sculpin Cottus girardi

Margined madtom Noturus insignis

Roseyface shiner Notropis rubellus

Comely shiner Notropis amoenus

Satinfin shiner (A) Cyprinella analostana

Spotfin shiner (A) Cyprinella spiloptera

Bluehead chub (A) Nocomis leptocephalus

Bull chub Nocomis raneyi

Fallfish (J&Y) Semotilus corporalis

Blacknose dace Rhinichthys atrastulus 

Pool-run guild

Tessellated darter Etheostoma olmstedi

Common shiner Luxilus cornutus

River chub (A&J) Nocomis micropogon

Fallfish (A) Semotilus corporalis

Cutlips minnow Exoglossum maxillingua 

Rosyside dace Clinostomus funduloides

Green sunfish (A&J) Lepomis cyanellus

White sucker Catostomus commersoni

Northern hog sucker Hypentelium nigricans

Pool-cover guild

Banded killifish Fundulus diaphanus

Swallowtail shiner Notropis procne

Spottail shiner Notropis hudsonius

Satinfin shiner (J&Y) Cyprinella analostana

Spotfin shiner (J&Y) Cyprinella spiloptera

Bluehead chub (Y) Nocomis leptocephalus

Bluntnose minnow (A) Pimephales notatus

Bluntnose minnow (J&Y) Pimephales notatus

Common carp Cyprinus carpio

Green sunfish (Y) Lepomis cyanellus

Pumpkinseed Lepomis gibbosus

Bluegill Lepomis macrochirus

Redbreast sunfish (A&J) Lepomis auritus

Redbreast sunfish (Y) Lepomis auritus

Largemouth bass Micropterus salmoides

Smallmouth bass (A&J) Micropterus dolomieu

Smallmouth bass (Y) Micropterus dolomieu

Rock bass (A&J) Ambloplites rupestris

Rock bass (Y) Ambloplites rupestris

Brown bullhead Ameiurus nebulosus

Yellow bullhead (A) Ameiurus natalis

Yellow bullhead (J&Y) Ameiurus natalis

Channel catfish Ictalurus punctatus

American eel Anguilla rostrata 
Habitat Classification 23

Table 11. Substrate codes used to classify the dominant 

and subdominant substrate within fish study reaches and 

hydraulic data-collection transects on the North Fork 

Shenandoah River, Virginia.

[cm, centimeters; n.a., not applicable; <, less than; >, greater than]

Code1 Description Sizes (cm)

01 Organic detritus n.a.

02 Vegetation n.a.

03 Silt < 0.006

04 Sand 0.006–0.2

05 Small gravel 0.2–0.8

06 Medium gravel 0.9–2.5

07 Large gravel 2.6–5.1

08 Small cobble 5.2–12.8

09 Large cobble 12.9–25.6

10 Small boulder 25.7–51.2

11 Large boulder > 51.2

12 Flat bedrock n.a.

13 Tilted bedrock n.a.

 1 From Trihey and Wegner, 1981; Platts and others, 1983;

Newcomb, 1992; and Bovee, 1997.

Table 13. Codes used to classify the percentage of fine particulate matter 

within a one square-meter area around a fish observation site, and within 

hydraulic data-collection transects on the North Fork Shenandoah River, 

Virginia.

[Fine particulate matter is defined as sand, silt and detritus.]

Code1

Fine 

particulate 

matter 

(Percent)

Description

1 0–25 Very few fines visible. If present, occur in very large interstitial spaces between large particles.

2 25–50 Fines present, filling large interstitial spaces. Few fines in smaller interstitial spaces.

3 50–75 Small particle interstitial spaces completely filled. Indistinct large particle boundaries.

4 75–100 Large and small materials nearly submerged in fines. Appears as sand bed with a few big rocks.

 1 From Trihey and Wegner, 1981; Platts and others, 1983; Newcomb, 1992;

and Bovee, 1997.

Table 12. Codes used to describe the cover found around 

a fish observation site and within hydraulic data-collection 

transects on the North Fork Shenandoah River, Virginia.

[cm, centimeters; >, greater than]

Code1 Description

01 No cover

02 Small-velocity shelter (12.9–25.6 cm)

03 Medium-velocity shelter (25.7–51.2 cm)

04 Large-velocity shelter (> 51.2 cm)

05 Dense cluster of small sticks

06 Undercut boulder or log that provides overhead cover

07 Log jam

08 Root wad

09 8.0–25.0-cm logs

10 Weed bed / Submerged aquatic vegetation

11 Bedrock formation

12 Complex cover

 1 From Trihey and Wegner, 1981; Platts and others, 1983;

Newcomb, 1992; and Bovee, 1997.
24 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Substrate variables for computing channel index values 

also were measured at each vertical along all transects of 

the six hydraulic data-collection reaches. The channel index 

values describe the study reach substrate, and are used as input 

for the North Fork Shenandoah River RHABSIM model.

Development of Fish Habitat-Suitability Curves 

HSC are interpreted using a suitability index, or rank, on 

a scale of 0–1, where 1 is the most utilized or preferred habitat. HSC developed in this study are river-specific to fish in the 

North Fork Shenandoah River, and are most appropriate when 

used for studies of that river. The development of fish HSC 

was based primarily on detailed fish-community sampling, 

habitat observations, and analysis of collected data. The HSC 

curves represent the variables used to represent the microhabitat suitable for fish within the North Fork Shenandoah River, 

and were used in the modeling phase of this research.

For the fish within the four fish guilds described, the 

measurements of water depth, water velocity, and channel 

index for each species were placed into suitability ranks based 

on the nonparametric tolerance limits (Murphy, 1948; Somerville, 1958; Slauson, 1988) for the central 50 percent, 75 

percent, and 90 percent of the data collected (Persinger, 2003). 

For example, for all the fish within one guild, the depths that 

represent the tolerance limits for the central 50 percent were 

ranked as 100-percent suitable, and received a value of 1. The 

depths that represent the tolerance limits for the central 75 

percent were ranked as 50-percent suitable, and received a 

value of 0.5. Those which represent the tolerance limits for the 

central 90 percent were used to establish the cutoff between 

suitable and unsuitable habitat, and received a rank of 0.2. 

The ranked habitat measures were summarized for each 

guild and used to create HSC for water depth, water velocity, and channel index for each fish guild (Persinger, 2003) 

(figs. 8–10). The fish sampling was completed during wadeable flows, so the habitat measures are most reliable for low 

to normal flows. Fish observations were not made in reaches 

that had water depths greater than 4 ft; therefore, the dataset 

used to create the fish HSC was not completely representative 

of the range of pool habitats found during the mesohabitat 

mapping. Consequently, the pool-cover guild depth-suitability 

curve developed by Persinger (2003) was altered for use in the 

modeling phase of this research so that all water depths greater 

than 4 ft were 100-percent suitable. No other alterations to the 

fish HSC were made. 

Canoeing Suitability Curves 

In addition to the fish HSC, depths and velocities suitable for recreation on the North Fork Shenandoah River were 

evaluated. HSC for canoeing were based only on water depths 

and velocities appropriate for canoeing (figs. 8-10) (Zappia 

and Hayes, 1998). Substrate or channel index was assumed 

100-percent suitable for all substrates (fig. 10).

Instream Flow Modeling to Determine 

Fish Habitat Availability

The program RHABSIM 2.0 for DOS and Windows 

(Thomas R. Payne and Associates, 1998) was used for calibration and simulation of flow and habitat. The RHABSIM modeling process includes two calibration phases and three simulation phases. The WSL and velocity calibrations are completed 

first, followed by WSL, velocity, and habitat simulations. 

Calibration and simulation phases were performed separately 

for each reach, then habitat simulation results were combined 

for each of the three river management sections. 

Model Calibration

The RHABSIM model calibration involves the datasets 

collected during the hydraulic data collection portion of the 

study. Calibration involves inputting topographic information 

for each study reach, WSLs, velocities, and discharge data for 

each hydraulic data-collection reach. The transect data is used 

to calculate stage-discharge ratings to enable simulation of 

depths and velocities for flows not measured during hydraulic 

data collection.

Inputs

For each reach and transect, the topographic elevation 

information derived from the horizontal and vertical surveys 

was input to the model as X, Y, Z coordinates. The X-value 

represents the distance along a transect from the headpin to 

the measurement vertical. The Y-value represents the distance 

upstream from the first transect. The most downstream transect has a Y-value of 0. The Z-value represents depth, and is 

calculated within the model from the bed elevation and WSL. 

Each X, Y, Z coordinate represents the middle point of one 

model cell for which a channel index value and three velocities 

were measured (appendix 1). The model cells within a transect 

represent an area half the distance to the next vertical in both 

directions, and a specified distance upstream and downstream 

of the transect.

In addition to cross-section elevation profiles for each 

transect, the model requires WSLs measured for each calibration discharge, average water-surface slope, and stage of zero 

flow (SZF) (appendix 1). Three best-estimate discharge measurements for each reach were used as calibration discharges 

in the RHABSIM model (table 9).

Water-Surface Elevation Calibration 

Three WSL calibration models are available through 

RHABSIM: step backwater, or water-surface profile (WSP), 

channel conveyance, or Manning stage-discharge (MANSQ), 

and log-log regression, regression of the log of the SZF and 

log of the best-estimate discharge (Thomas R. Payne and 
Instream Flow Modeling to Determine Fish Habitat Availability 25

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Figure 8. Fish habitat depth-suitability curves for riffle (A), fast-generalist (B), pool-run (C), and pool-cover guilds (D), 

and canoeing habitat depth-suitability curve (E) for the North Fork Shenandoah River, Virginia. Fish habitat suitability 

curves based on data from Persinger, 2003.
26 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

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Figure 9. Fish habitat velocity-suitability curves for riffle (A), fast-generalist (B), pool-run (C), and pool-cover guilds (D), 

and canoeing habitat velocity-suitability curve (E) for the North Fork Shenandoah River, Virginia. Fish habitat suitability 

curves based on data from Persinger, 2003.
Instream Flow Modeling to Determine Fish Habitat Availability 27

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Figure 10. Fish habitat channel index-suitability curves for riffle (A), fast-generalist (B), pool-run (C), and pool-cover fish 

guilds (D), and canoeing habitat channel index-suitability curve (E) for the North Fork Shenandoah River, Virginia. Fish 

habitat suitability curves based on data from Persinger, 2003.
28 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Associates, 1998; U.S. Geological Survey, 2001). WSL models were selected for each reach based on reach habitat conditions and hydraulic properties (table 14). Each model used 

the measured (observed) WSL, calibration discharges, and 

n-values or beta-values (as specified by the particular model) 

to produce a simulated WSL. The model calibration was an 

iterative process, with new n-values or beta-values selected to 

minimize the difference between the observed and simulated 

WSL (U.S. Geological Survey, 2001). For most transects, the 

difference between observed and simulated WSL was less than 

0.05 ft (appendix 1). When the differences were as great as 

0.08 ft, transects were located within riffle habitats with steep 

water-surface slopes, or along steep streambanks where WSL 

measurements were difficult. 

When the WSL model calibration parameters were finalized and the WSLs had been simulated for the calibration 

discharges, the model was used to simulate WSLs for a set of 

30 discharges representative of the flows within each management section of the river (table 15). The model simulation 

flows were corrected for drainage area differences between the 

hydraulic data-collection reach and the station with which it is 

associated (table 16). For example, at Route 648, the drainage 

area is 3.7 percent less than the drainage area at the Strasburg 

station; therefore, to represent 300 ft3/s discharge at the Strasburg station, an equivalent discharge of 289 ft3

/s was simulated 

in the RHABSIM model. 

Velocity Calibration 

Three methods are available within RHABSIM for velocity calibration: 1-velocity, regression, or depth. Various velocity calibrations and simulations were run to compare observed 

and simulated velocities, with the 1-velocity method selected 

for all reaches and transects. The velocity dataset that produced the least difference between the best-estimate discharge 

and model-calculated discharge was selected as the primary 

dataset to calibrate the velocity model (table 17). The selected 

dataset was generally the velocity dataset for the highest 

calibration discharge. The velocity model calculates a transect 

discharge using observed velocities and calculated depths from 

the difference between the WSL and channel bed elevations. 

The transect discharge is compared with calibration discharges 

for the reach to obtain velocity adjustment factors (VAF). VAF 

are used to simulate velocity for the 30 simulation flows.

Habitat Simulation and Development of 

Weighted Usable-Habitat Area Curves 

The WSL and velocity simulations and the fish and 

canoeing HSC were input to the Habitat Simulation Model 

(HABSIM) (Thomas R. Payne and Associates, 1998). HABSIM calculates a composite suitability index (SI) for each 

model cell by evaluating the simulated attributes (water 

depths, water velocities, and channel index values) against the 

HSC (U.S. Geological Survey, 2001). Multiplicative aggregation (U.S. Geological Survey, 2001) was used to calculate the 

SI for each cell. SI for all cells within a reach were summed 

for a total weighted usable-habitat area (WUA). The process 

was repeated for each guild and canoeing over 30 simulation 

flows, and a functional relation between habitat and discharge 

was defined and expressed in the form of WUA curves.

As with the mesohabitat classification, the North Fork 

Shenandoah River basin was divided into upper, middle, and 

lower sections that are associated with the streamflow-gaging stations (Cootes Store, Mount Jackson, Strasburg) near 

the downstream end of each section. From one station to the 

next downstream, the drainage area for each station more than 

doubles (table 1) (U.S. Geological Survey, 2003). The median 

annual exceedance flows increase approximately two-fold 

from one station to the next downstream (61 ft3/s, 182 ft3/s, 

and 310 ft3/s for the Cootes Store, Mount Jackson, and Strasburg stations, respectively). The distance between streamTable 14. Water-surface calibration method used in RHABSIM for each hydraulic data-collection reach on 

the North Fork Shenandoah River, Virginia.

[When two methods are listed, one method was used for the first transect and another method was used for the rest of the

transects. RHABSIM, River Habitat Simulation Model; WSL, water-surface elevation; ft3/s, cubic feet per second; WSP,

water-surface profile method; MANSQ, Manning stage-discharge method; Log-log regression, regression of the log of

the stage zero flow and log of the best-estimate discharge]

Hydraulic Reach WSL calibration method1 Calibration discharge (ft3/s)

Plains Mill Log-log regression all

Laurel Hill Farms MANSQ 400

Spring Hollow MANSQ 432

Posey Hollow Log-log regression cross section 1, WSP 666

Route 648 Log-log regression cross section 1, WSP 86.98

Winchester Dam Log-log regression cross section 1, WSP 218

 1 Thomas R. Payne and Associates, 1998.
Instream Flow Modeling to Determine Fish Habitat Availability 29

Table 15. Simulation flows for the hydraulic data-collection reaches in the upper, middle, and lower management 

sections of the North Fork Shenandoah River, Virginia

[Equivalent flow, flow at each reach that was adjusted by drainage area to represent flow at the station; Bold values represent calibration 

discharges; ft3/s, cubic feet per second.]

Upper management section Middle management section Lower management section

Cootes Store Plains Mill Mount Jackson Laurel Hill 

Farms Strasburg Spring Hollow

Posey 

Hollow Route 648 Winchester Dam

Flow

(ft3/s)

Equivalent 

flow

(ft3/s)

Flow

(ft3/s)

Equivalent 

flow

(ft3/s)

Flow

(ft3/s)

Equivalent 

flow

(ft3/s)

Equivalent 

flow

(ft3/s)

Equivalent 

flow

(ft3/s)

Equivalent 

flow

(ft3/s)

0.2a 0.3 1b 1 25c 23 24 24 30

0.5 .8 2 3 35 32 33 34 42

1 2 4 5 45 41 43 43 54

2 3 6 8 55 50 53 53 66

4 6 8 10 65 59 62 63 79

6 9 10 13 75 68 72 72 91

8 12 15 19 87 78 83 83.3 105

10 15 20 26 90 81 86 87.0 109

15 22.5 25 32 105 94.4 100 101 127

20 30 35 45 128 115 122 123 155

25 38 45 58 141 126 135 136 170

30 46 55 71 162 146 155 156 195

35 53 65 83 180 162 172 173 218

40 61 73 93.8 230 207 219 221 278

45 68 85 109 275 248 263 265 332

50 76 94 120 300 270 287 289 363

60.75 92.5 110 141 350 315 335 337 423

71.7 109 130 167 375 338 359 361 453

80 121 150 192 400 360 383 385 484

90 137 175 224 461 415 441 444 557

100 152 200 256 480 432 459 462 580

120 183 235 301 500 450 479 482 605

173.5 264 275 353 546 491 523 526 654

202.4 308 312 400 575 518 550 554 696

249 379 350 449 600 540 574 578 725

288 438 400 513 650 585 622 626 786

350 533 450 577 696 626 666 670 841

400 609 500 641 800 720 766 770 967

450 685 525 673 900 810 861 867 1,088

500 761a 550 705b 1,180 1,062 1,129 1,136 1,430c

 a The simulation discharges for the upper management section represent a range between the lowest historic mean daily flow recorded at 

Cootes Store, and 1.74 times the highest measured flow at the Plains Mill study reach.

 b The simulation discharges for the middle management section represent a range between 0.55 times the lowest historic mean daily flow 

recorded at Mount Jackson, and 1.76 times the highest measured flow at the Laurel Hill farms study reach.

 c The simulation discharges for the lower management section represent a range between 0.75 times the lowest historic mean daily flow 

recorded at Strasburg, and the highest measured flow at the Winchester Dam study reach.
30 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Table 16. Drainage-area-based correction factors for relating 

discharge measured at hydraulic data-collection reaches to 

discharge measured at streamflow-gaging stations on the 

North Fork Shenandoah River, Virginia.

[Simulated discharges for each streamflow-gaging station were multiplied 

by the percent difference in drainage area between the station and the 

ungaged reach to correct for flow differences.]

River management section

and associated streamflowgaging stationReach

Drainage area 

difference 

(percent)

Upper–Cootes Store Plains Mill 53.2

Middle–Mount Jackson Laurel Hill Farms 28.2

Lower–Strasburg Spring Hollow -10.0

Lower–Strasburg Posey Hollow -4.3

Lower–Strasburg Route 648 -3.7

Lower–Strasburg Winchester Dam 20.9

Table 17. Velocity calibration discharges 

used in RHABSIM for each hydraulic datacollection reach and transect on the North Fork 

Shenandoah River, Virginia.

[RHABSIM, River Habitat Simulation Model; ft3/s, 

cubic feet per second]

Reach Transect

Calibration 

discharge 

(ft3/s)

Plains Mill 1a, 5 379

Plains Mill 2, 3b, 4 264

Plains Mill 3, 3a, 7 308

Plains Mill 6 438

Laurel Hill Farms 1–5 400

Spring Hollow 1–5 432

Posey Hollow 1–5 666

Route 648 1, 6, 8 444

Route 648 2, 3, 5, 7 526

Route 648 4 136

Winchester Dam 1–3 1,430 flow-gaging stations and substantial increases in drainage area 

and discharge support the decision to run RHABSIM model 

simulations for three sections of the river.

The habitat-discharge relation for the upper management 

section was created using data collected at the Plains Mill 

reach. The flows were corrected for drainage area differences 

between the Cootes Store station and the reach (tables 15 and 

16), and transects were weighted to represent mesohabitat 

percentages in the upper section of the North Fork Shenandoah River (appendix 1). The Plains Mill reach contains nine 

transects which were placed in riffle, pool, and run habitats 

with a variety of substrate and cover types (table 8). The complex nature of the reach and variety of water-surface slopes 

made it difficult to calibrate, so modeling results may not be as 

representative as results for the more downstream sections.

The habitat-discharge relation for the middle management section was created using data collected at the Laurel 

Hill Farms reach. The flows were corrected for drainage area 

differences between the Mount Jackson station and the reach 

(tables 15 and 16), and transects were weighted to represent 

mesohabitat percentages in the middle section of the North 

Fork Shenandoah River (appendix 1). Laurel Hill Farms was 

the only reach near the Mount Jackson station. Transects were 

placed only in riffles and runs in this reach; therefore, the 

WUA curves are most representative of these mesohabitats. 

The habitat-discharge relation for the lower management 

section was created using data collected at the Spring Hollow, 

Posey Hollow, Route 648, and Winchester Dam reaches. The 

flows were corrected for drainage area differences between 

the Strasburg station and each reach (tables 15 and 16), and 

transects were weighted to represent mesohabitat percentages in the lower section of the North Fork Shenandoah River 

(appendix 1). 

Transect weighting factors are used in RHABSIM to 

ensure that the amount of habitat represented by each reach 

corresponds to the amount of mesohabitat in that section of the 

river (appendix 1). For the upper section, Plains Mill transects 

were weighted to represent the percentages of riffles, runs, and 

pools in that section (table 6). The middle section weighting 

factors were assigned in the same way. For the lower section, weighting factors were distributed among all transects 

in the four reaches to accurately represent the mesohabitat 

percentages in that section (table 6). Riffle habitat is present 

in the Posey Hollow, Spring Hollow, and Route 648 reaches; 

therefore, weighting factors were distributed among all riffle 

habitats in the three reaches. Most of the pool habitat within 

the study reaches in the lower section was artificial pool 

located in the Winchester Dam site. In an effort to include 

transects that represent natural pools, pocket run habitat was 

grouped with pool habitat. In general, depths in the holes of 

pocket runs were closer to the range of depths for pools than 

runs. The pool habitat was represented by transects in the 

Winchester Dam and Route 648 reaches, and run habitat represented by transects in Posey Hollow, Spring Hollow and Route 

648 reaches. Because simulation flows had been corrected 

for drainage area and transects weighted for lower section 

mesohabitat, the resulting individual WUA curves from all 

four reaches could be combined to produce a composite set of 

WUA curves for the lower management section. 
Instream Flow Modeling to Determine Fish Habitat Availability 31

Habitat-Discharge Relations for the 

Management Sections

The habitat-discharge relations for the upper and middle 

sections of the North Fork Shenandoah River are each derived 

from one study reach, but the relations for the lower management section represent a composite of four study reaches. For 

the lower section, each reach was modeled individually and 

WUA summed, so the WUA will be greater in magnitude 

than in the upper and middle sections. For management and 

comparison purposes, however, the general trend of the WUA 

curves is more important than the magnitude. The magnitude 

reflects the WUA in the study reaches, but is not directly representative of the actual WUA in the rest of river. The WUA 

for each river management section is represented by four 

habitat-discharge relations for fish: riffle guild, fast-generalist 

guild, pool-run guild, and pool-cover guild, and one habitatdischarge relation for canoeing. These relations consist of the 

simulated discharge and corresponding habitat value (tables 

18–20, figs. 11–13).

The canoeing-discharge relations are slightly different 

than the fish habitat-discharge relations. Canoeing suitability 

was evaluated based upon depths and velocities, with all substrates assumed suitable (Fig. 10). 

The RHABSIM modeling and data analysis resulted in 

a series of graphs, or WUA curves, that illustrate relations 

between discharge and habitat area. The highest point, or 

peak, for each WUA curve represents the discharge with the 

maximum WUA for each guild analyzed. Each guild will have 

slightly different maximum WUA, based on the fish HSC 

evaluated and the microhabitat conditions of each study reach. 

Therefore, the discharge with the maximum WUA for one 

guild may not represent the maximum WUA for other guilds. 

The maximum, inflection points, and percentiles of the WUA 

curves are typically evaluated as potential flow targets at the 

level of protection desired, or as points above which greater 

amounts of flow only provide minor gains in usable habitat (Sutton and Morris, 2004). At any point in time, a given 

streamflow may be more suitable for some species or lifestages but less suitable for others. In streams with more than 

one species of interest, the challenge is to evaluate the effects 

of any recommended flows on all species (Sutton and Morris, 

2004).

A relatively simple analysis would identify the peak of 

the WUA curve as a flow target, regarding more habitat as 

desirable and less habitat as undesirable. The relation between 

discharge and habitat is complex; however, and it is important to understand the factors that affect WUA amounts and 

the relation between WUA and the hydrologic regime. WUA 

is consistently low during high flows, increases as flows 

decrease to normal or low-flow conditions, then decreases 

during extreme low-flow conditions. These general patterns 

are explained partially by considering the fish HSC for depth 

and velocity. The right side of the curves represents high flows 

having deep water depths and fast velocities, conditions which 

are not ranked as highly suitable for any fish guilds. As flows 

decrease, water depths and water velocities decrease, creating 

habitat conditions that are ranked suitable for more species—

typically pool-cover and pool-run guilds. As flows continue 

to decrease, depths and velocities become more suitable to all 

guilds, and the WUA increases up to the maximum. The flows 

associated with the maximum WUA are different for each 

guild within each management section. For fish guilds that 

have shallow water depths rated highly suitable, lower flows 

can provide more habitat. At some point, each fish guild will 

be limited by water depths or velocities (or lack thereof), and 

WUA curves will sharply decrease. Flows with shallow water 

depths and either fast or slow water velocities are represented 

on the left side of the curves, and represent a decrease in habitat suitability and availability. 

 The WUA curves are compared to the natural hydrograph to understand the relations between habitat suitability 

and the distribution of streamflows within and between years. 

The WUA curves represent the habitat associated with the 

range of simulated flows, regardless of month or season. 

Within one year, for example, normal summer flows may not 

provide the maximum WUA that could be obtained during spring flows. During dry years flows that provide the 

maximum WUA may not be attainable, or will be much less 

frequent than during wet years (Sutton and Morris, 2004). 

Understanding the frequency of flows that provide WUA 

should provide a framework for assessing future habitat conditions during seasons, and during wet, normal, and dry years. 

Upper Section

For the upper management section near the Cootes Store 

station, WUA (fig. 11) was simulated for flows between 0.2 

and 500 ft3/s. The range of simulation flows represents flows 

much higher and lower than the normal range of flows for 

July, August, and September (4.4–40 ft3/s) to adequately 

describe the relation between habitat and discharge. Three out 

of four guilds have limited WUA at high flows in the range 

of 300–500 ft3/s. The pool-cover guild WUA is not limited at 

high flows. During high-flow periods the majority of the main 

channel has low WUA for the riffle, fast-generalist, and poolrun guilds. Water velocities and depths are much greater during periods of high flow, and fish and other aquatic organisms 

may move to edge areas to find shelter from swift velocities. 

During moderate to low flows, the WUA for the riffle and 

fast-generalist guilds appears to be more abundant than for the 

pool-run and pool-cover guilds. 

The upper section of the North Fork Shenandoah River 

shows more variation in the habitat-discharge relation among 

guilds than the other two downstream sections. For the upper 

management section, flows that sustain maximum WUA are 

close to 42 ft3/s for all guilds, a flow that approximately correlates to the 25-percent exceedance flow for July, August, 

and September. The pool-cover and pool-run WUA curves are 

similar in shape (fig. 11). WUA for these two guilds gradually 

increases as flows decline from the highest simulated flow, 

500 ft3/s, to 100 ft3/s. Flows between 100 and 40 ft3/s provide 
32 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Table 18. Weighted usable-habitat area in square feet per 1,000 feet of stream 

for the upper management section of the North Fork Shenandoah River, Virginia.

[ft3/s, cubic feet per second]

Cootes Store

discharge

(ft3/s)

Fish guild

Canoeing

Riffle Fast-generalist Pool-run Pool-cover

0.2 0 0 0 0 0

0.5 124 0 43 29 0

1 312 19 688 151 0

2 1,715 702 1,322 423 9

4 4,251 1,989 3,140 1,929 457

6 5,575 5,873 6,030 3,593 1,419

8 8,320 7,769 6,957 5,101 2,701

10 10,524 8,765 8,046 6,462 3,978

15 14,124 12,620 10,598 8,683 6,769

20 17,088 15,373 12,410 10,946 9,634

25 19,361 17,307 13,551 12,860 12,470

30 20,808 20,011 14,915 14,803 15,381

35 21,553 21,736 15,884 16,243 18,231

40 22,342 22,851 16,376 17,747 21,240

45 20,355 23,326 16,524 18,367 24,198

50 19,001 24,919 17,419 19,446 27,202

60.75 17,693 24,901 17,507 19,654 33,814

71.7 16,161 22,764 17,211 19,845 40,682

80 14,711 22,760 16,933 20,216 46,072

90 12,556 21,244 16,987 19,547 53,117

100 11,478 19,615 16,139 19,681 59,231

120 9,094 16,304 13,134 19,450 70,361

173.5 3,350 10,875 9,811 17,649 88,676

202.4 2,239 8,008 7,532 17,454 94,775

249 1,235 4,113 5,652 14,958 101,531

288 564 2,528 3,691 12,670 104,497

350 272 1,054 2,261 10,904 105,945

400 54 645 1,846 8,622 104,805

450 54 389 1,382 7,103 102,642

500 22 151 919 6469 100,359
Instream Flow Modeling to Determine Fish Habitat Availability 33

Table 19. Weighted usable-habitat area in square feet per 1,000 feet of stream for 

the middle management section of the North Fork Shenandoah River, Virginia.

[ft3/s, cubic feet per second]

Mount Jackson 

discharge

(ft3/s)

Fish guild

Canoeing

Riffle Fast-generalist Pool-run Pool-cover

1 25 25 86 561 0

2 143 62 307 1,683 10

4 184 150 658 3,641 155

6 518 358 1,070 5,934 436

8 848 420 1,464 6,933 983

10 944 457 1,702 7,779 1,735

15 1,891 1,108 2,513 9,533 4,502

20 2,466 1,644 3,281 11,870 8,387

25 4,180 2,839 4,114 12,099 12,550

35 5,743 3,745 5,679 14,438 20,705

45 5,997 5,101 6,963 14,861 28,495

55 6,561 6,141 7,812 16,157 36,228

65 6,832 6,849 8,486 17,324 43,323

73 7,136 7,071 9,582 16,559 48,684

85 7,489 7,138 9,751 16,939 55,503

94 7,560 7,219 9,616 14,942 60,019

110 7,511 6,646 9,391 13,678 67,690

130 7,390 5,872 9,141 12,078 75,309

150 6,320 5,929 8,842 10,465 81,857

175 5,424 5,311 8,392 9,376 88,058

200 3,548 4,324 7,640 7,490 93,084

235 2,782 2,316 6,132 6,506 98,963

275 2,113 1,970 5,156 4,858 104,146

312 1,321 1,306 4,716 4,443 107,258

350 1,030 690 3,553 3,959 109,685

400 630 549 2,387 2,622 111,942

450 433 356 1,645 2,066 113,299

500 282 306 1,306 1,929 113,684

525 282 306 1,163 1,919 113,401

550 282 306 951 1,566 112,487
34 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Table 20. Weighted usable-habitat area in square feet per 1,000 feet of 

stream for the lower management section of the North Fork Shenandoah 

River, Virginia.

[ft3/s, cubic feet per second]

Strasburg

discharge

(ft3/s)

Fish guild

Canoeing

Riffle Fast-generalist Pool-run Pool-cover

25 9,544 7,592 17,321 7,525 6,932

35 12,920 11,002 22,423 8,098 11,090

45 15,245 13,902 26,750 8,405 18,132

55 15,550 15,061 28,760 9,671 28,418

65 16,788 16,358 30,733 12,844 42,044

75 17,157 17,225 32,557 12,975 59,288

87 17,782 18,300 33,617 13,522 83,836

90 17,849 18,482 33,051 13,654 90,634

105 18,551 18,498 32,728 14,144 120,425

128 18,229 17,162 31,793 14,493 172,104

141 18,035 16,716 30,509 14,813 199,798

162 15,709 12,288 26,412 14,829 248,441

180 14,664 11,920 25,468 14,726 288,750

230 11,859 11,359 23,620 14,916 369,386

275 10,224 9,169 22,117 15,185 415,184

300 7,776 7,005 21,143 15,470 427,793

350 4,464 5,012 17,530 15,517 441,082

375 4,016 4,722 16,331 15,090 444,836

400 3,613 4,216 15,075 14,378 447,465

461 2,231 2,409 12,903 10,984 449,179

480 1,889 1,988 12,426 10,957 451,667

500 1,786 1,905 11,510 10,771 452,527

546 1,316 1,626 9,310 10,670 454,895

575 1,149 1,286 8,619 10,575 456,922

600 1,208 1,103 8,223 10,521 458,343

650 884 906 6,531 9,592 460,612

696 781 753 5,993 8,590 461,278

800 274 624 4,015 7,564 462,742

900 238 537 2,795 6,961 461,047

1,180 118 216 1,364 5,515 435,799
Instream Flow Modeling to Determine Fish Habitat Availability 35 ������������ ��������������������� �������������� ���������������� ��������������������������������� ������������������������������� ��������� ���������������������������� ������������������������������� ������������������������������� ������������������������������ ����������� �����������������������������������

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Figure 11. Weighted usable-habitat area for the upper management section of the North Fork Shenandoah River, Virginia.
36 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

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Figure 12. Weighted usable-habitat area for the middle management section of the North Fork Shenandoah River, Virginia.
Instream Flow Modeling to Determine Fish Habitat Availability 37

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Figure 13. Weighted usable-habitat area for the lower management section of the North Fork Shenandoah River, Virginia.
38 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

the maximum and constant amount of WUA for pool-cover 

and pool-run guilds; WUA sharply decreases with flows less 

than 40 ft3/s. Fast-generalist WUA (fig. 11) steeply increases 

as flows decline from 500 to 60 ft3/s. Flows between 60 and 

50 ft3/s provide the maximum WUA, and then WUA sharply 

decreases with flows less than 40 ft3/s. Riffle guild WUA 

(fig. 11) gradually increases as flows decrease from the highest simulated flow to 40 ft3

/s, which is the flow with the maximum WUA. At flows less than 40 ft3

/s riffle WUA declines. 

Riffle WUA remains the most abundant of all four guilds in 

the upper management section. WUA is limited at and below 

the 90-percent exceedance flow (1.6 ft3/s) (fig. 11).

To illustrate the amount of WUA commonly expected 

for each guild during the low-flow period, the normal range 

of flows (4.4–40 ft3/s), the 50-percent exceedance flow (14 

ft3/s), and the 90-percent exceedance flow (1.6 ft3/s) for July, 

August, and September flows were plotted over each set of 

WUA curves (fig. 11). The normal range of flows for July, 

August, and September only includes the maximum WUA for 

the riffle guild. During the low-flow period it is common for 

the actual WUA to be less than the maximum simulated WUA 

in late summer and early fall for all guilds. With the steep 

decline in WUA within the normal range of flows during July, 

August, and September, it is also likely that habitat conditions 

are dynamic during the low-flow period in the upper section of 

the North Fork Shenandoah River. 

For the upper management section, canoeing suitability 

is at a maximum at 350 ft3/sec. At this flow riffles, runs, and 

pools have suitable depths and velocities for canoeing. At 100 

ft3/sec approximately half the amount of canoeing WUA is 

available than is with 350 ft3/sec. During summer, these flows 

occur less than 25-percent of the time based on the exceedance 

flows for July, August, and September (table 2). 

Middle Section

For the middle management section near the Mount Jackson station, WUA (fig. 12) was simulated for flows between 1 

and 550 ft3/s. The range of flows represents flows much higher 

and lower than the normal range of flows for July, August, and 

September (47–155 ft3/s) to adequately describe the relation 

between habitat and discharge. For all four fish guilds WUA 

is limited at high flows in the range of 300–550 ft3/s because 

the water depths and velocities are outside the suitable range. 

During moderate and low flows habitat is abundant in similar 

amounts for all four fish guilds. 

The middle management section of the North Fork 

Shenandoah River shows little variation in the habitat-discharge relations for all four guilds. The flows that sustain 

maximum WUA for all guilds are between 70 and 80 ft3/s, a 

flow that approximately correlates with the 50-percent exceedance flow for July, August, and September. For all guilds, as 

flows declined from highest measured flow, 550 ft3/s, to 80 

ft3/s, WUA steeply increases. WUA decreases with flows less 

than 75 ft3/s, and is highly limited at and below the 99-percent 

exceedance flow (8 ft3/s).

There is more WUA for the pool-cover guild than for 

the three other fish guilds in the middle management section. 

Depths, velocities, and substrates were most suitable to fish 

in the pool-cover guild (fig. 12); however, fish from the other 

guilds are also supported. It is possible that substrate and cover 

suitability may be a limiting factor for the riffle, fast-generalist, and pool-run guilds in the middle section, but not for the 

pool-cover guild.

To illustrate the amount of WUA commonly expected 

for each guild during the low-flow period, the normal range of 

flows (47–155 ft3/s), the 50-percent exceedance flow (78 ft3/s), 

and the 90-percent exceedance flow (30 ft3/s) for July, August, 

and September flows were plotted over each set of WUA 

curves (fig. 12). Unlike the upper and lower sections, the normal range of flows for July, August, and September includes 

the maximum WUA for all fish guilds in this section. Within 

this range, the WUA does not change much with changes in 

flow. At flows less than the 75-percent exceedance flow, WUA 

decreases at a similar rate for all guilds.

For the middle management section, canoeing suitability 

is at a maximum at 500 ft3/sec. At 100 ft3/sec approximately 

half the amount of canoeing WUA is available than is with 

500 ft3/sec. During summer, these flows occur more than 50-

percent of the time based on the exceedance flows for July, 

August, and September (table 2).

Lower Section

For the lower management section near the Strasburg station, WUA (fig. 13) was simulated for flows between 25 and 

1,180 ft3/s. The range of flows represents flows much higher 

and lower than the normal range of flows for July, August, and 

September (119–283 ft3/s) to adequately describe the relation 

between habitat and discharge. For all four fish guilds, the 

WUA is limited at high flows in the range of 500–1,180 ft3/s. 

As with the upper section during high-flow periods, edge and 

backwater areas contain suitable habitat, but the majority of 

the main channel sustains small amounts of WUA. During 

moderate and low-flow periods habitat for pool-cover and 

pool-run is most abundant. 

For the riffle, fast-generalist, and pool-run guilds of the 

lower section of the North Fork Shenandoah River, flows 

that sustain maximum WUA range between 90 and 100 ft3/s 

(fig. 13), which approximately correlates to the 90-percent 

exceedance flow for July, August, and September. The WUA 

for these three guilds increases from the highest simulated 

flow, 1180 ft3/s, to 100 ft3/s. With flows below 90 ft3/s WUA 

decreases more gradually than the upper or middle sections. 

For the pool-cover guild, WUA is at a maximum at 500 ft3/s, 

and is maintained at a constant level with only slight decreases 

between 500 and 65 ft3/s. WUA for the pool-cover guild 

decreases steeply between 65 and 25 ft3/s. For the lower section, the amount of WUA, represented by the magnitude or 

height of the curves, is substantially greater for the pool-run 

guild than for the other three guilds. WUA for all fish guilds is 

limited below the 99-percent exceedance flow (56 ft3/s). 
Instream Flow Modeling to Determine Fish Habitat Availability 39

 To illustrate the amount of WUA commonly expected 

for each guild during the low-flow period, the normal range 

of flows (119–283 ft3/s), the 50-percent exceedance flow (171 

ft3/s), and the 90-percent exceedance flow (87 ft3/s) for July, 

August, and September flows were plotted over each set of 

WUA curves (fig. 13). The normal range of flows for July, 

August, and September does not include the maximum WUA 

for any guild. Habitat appears to be more abundant for flows 

less than the 75-percent exceedance flow. However, the habitat 

may be composed of mostly disconnected patches and edge 

areas, and the potential water-quality problems within the shallow habitats make the habitat suitability questionable.

For the lower management section, canoeing suitability is 

at a maximum at 800 ft3/sec. At 162 ft3/sec approximately half 

the amount of canoeing WUA is available than is with

800 ft3/sec. During summer, these flows occur more than 50-

percent of the time based on the exceedance flows for July, 

August, and September (table 2). 

Time-Series Analysis for Low-Flow Periods 

A time-series analysis was completed to overlay the habitat-discharge relations on the entire historic streamflow record 

to show how WUA may have fluctuated daily, seasonally, and 

during low-flow periods. Two different withdrawal scenarios 

were simulated to show how WUA may be affected by various 

water-withdrawal practices.

Discharge data for each of the three stations were 

obtained (U.S. Geological Survey, 2003) for the period of 

record through water year 2001 (ending September 30, 2002). 

To simulate the withdrawal scenarios, discharge datasets were 

created from the historic data to represent streamflows with 

zero water withdrawals and double water withdrawals for each 

management section. 

No major dams are present on the North Fork Shenandoah River; therefore, the primary way that humans affect 

instream flows is related to water withdrawals and returns 

for municipal, industrial, and agricultural uses. Water suppliers, cities, counties, industries, farmers, and individuals 

report their monthly water use to the Virginia Department of 

Environmental Quality (DEQ). Reported agricultural water 

use is much lower than municipal and industrial water use 

in the North Fork Shenandoah River basin (Virginia DEQ, 

written commun., February 15, 2005). Agricultural withdrawals in Virginia are reported on a volunteer, survey basis, so 

the accuracy of the values is uncertain. The reported surfacewater withdrawals for agriculture have occurred in June, July, 

August, and September in the North Fork Shenandoah River 

basin. Based on five years of data (1998-2002), the average 

daily water withdrawals on the North Fork Shenandoah River 

for all uses are 3.0 ft3/s, 0.3 ft3/s, and 14.5 ft3/s for the upper, 

middle, and lower management sections respectively. Due to 

the general nature of the location information for water withdrawals, the middle management section does not appear to 

have large withdrawal volumes. The 0.3 ft3/s value is likely too 

low, but is the best estimate available at present. 

The average daily water withdrawals (1998-2002) were 

added back to the historic daily mean flow data for the months 

of June, July, August, and September to create a zero waterwithdrawal scenario (in which no water is removed from the 

river). For each respective section of the river, withdrawal 

amounts were added cumulatively (3.0 ft3/s, 3.3 ft3/s, and 

17.8 ft3/s). This scenario simulates the potential success of 

water conservation measures in maintaining WUA during 

low-flow periods. The second flow scenario involves doubling 

water withdrawals to simulate the potential effects of increased 

water use on WUA. The cumulative daily withdrawal values were subtracted from the historic daily mean flow data. 

Because the discharge data already includes current water 

withdrawals, subtracting withdrawal amounts of 3.0 ft3/s, 3.3 

ft3/s, and 17.8 ft3/s from respective management sections represents a doubling of water use. 

The discharge datasets and habitat-discharge relations 

were entered into and evaluated with a time-series analysis 

spreadsheet (James Henriksen, U.S. Geological Survey, written comun., 2002). The spreadsheet contains algorithms to 

assign the WUA value to each daily mean flow value for the 

historic period. The time-series analysis produces simulated, 

daily variations of WUA for the entire period of record. For 

dry years noted earlier (Historic Flow Summary) the timeseries results were examined to identify flows that limit the 

WUA for fish and to identify fish guilds that are most affected. 

The time-series results were also examined to identify and 

describe the range of habitat conditions for each fish guild. 

The habitat time-series analysis shows the daily and 

seasonal variation of habitat with flow, as well as times when 

WUA is limited during dry periods (figs. 14-16). Flow is 

closely linked to habitat availability, and during dry months 

(approximately July through November), a decrease in flow 

generally corresponds to a decrease in WUA, and an increase 

in flow corresponds to an increase in WUA. This habitat area 

increase may occur because during low flows, an increase due 

to rainfall or run-off creates more moderately shallow areas of 

run and riffle habitat. During wet months of the year (approximately December through June), increases in flow (peaks of 

the hydrograph) frequently correspond to decreases in WUA. 

This WUA decrease may occur because during high flows, 

riffles and runs are inundated and much of the river becomes 

run habitat with fast velocities, which is not suitable for many 

species. 

The flow corresponding to the maximum WUA represents a boundary between whether WUA increases or 

decreases with increased flow. When flows are lower than 

the flow corresponding to the maximum WUA, and there is 

an increase due to rainfall or run off, WUA increases. When 

flows are higher than the flow corresponding to the maximum 

WUA, and there is an increase due to rainfall or run off, WUA 

decreases. A flow roughly corresponding to the maximum 

WUA for all guilds was selected and is noted on each timesseries graph (figs. 14-16).
40 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

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Figure 14. Daily mean discharge and weighted usable-habitat area (WUA) for fish guilds in the 

upper management section of the North Fork Shenandoah River, Virginia for the 1930 low-flow

period (A), 1964 low-flow period (B), and 1999 low-flow period (C). Discharge associated with the 

maximum WUA for all fish guilds in this section of the river is indicated.
Instream Flow Modeling to Determine Fish Habitat Availability 41

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Figure 15. Daily mean discharge and weighted usable-habitat area (WUA) for fish guilds in the middle 

management section of the North Fork Shenandoah River, Virginia for the 1964 low-flow period (A), 1999 

low-flow period (B). Discharge associated with the maximum WUA for all fish guilds in this section of the 

river is indicated.
42 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

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Figure 16. Daily mean discharge and weighted usable-habitat area (WUA) for fish guilds in the lower 

management section of the North Fork Shenandoah River, Virginia for the 1930 low-flow period (A), 1964 

low-flow period (B), and 1999 low-flow period (C). Discharge associated with the maximum WUA 

for all fish guilds in this section of the river is indicated.
Instream Flow Modeling to Determine Fish Habitat Availability 43

 The magnitude of habitat decline during natural dry 

periods can be seen in the time-series habitat values associated 

with extreme low flows recorded for the upper section of the 

North Fork Shenandoah River (fig. 14). The maximum WUA 

is available at a range between 40 and 55 ft3/s for all four fish 

guilds. The 40 ft3/s flow marked on figure 14 indicates the 

boundary below which WUA decreases with decreases in flow. 

This flow is equivalent to the 25-percent exceedance flow for 

the low-flow period and is the upper end of the normal range 

of flows for July, August, and September. The time-series 

graphs show that during extended periods with flows much 

lower than the normal range of flows, habitat can be highly 

limited (fig. 14). 

In the upper management section, the fast-generalist and 

pool-cover guilds showed the greatest response to decreases in 

flow. The WUA for these two guilds was lowest during July, 

August, and September of 1930, 1963, and 1964, and during 

July and August of 1999 (fig. 14). The WUA for the fast-generalist guild decreased more than that for other guilds during 

previous low-flow periods. This implies that run habitat and 

run-dwelling fish species in the upper management section are 

most vulnerable to habitat loss during low-flow periods. Were 

water-withdrawals to increase during these times in the upper 

section, habitat conditions would be limited more frequently. 

During wet months (December-June), WUA is relatively 

constant and sustained. With large rain events WUA for riffle 

and fast-generalist guilds decline, probably indicating that 

the habitats are washed out in deep, fast flows. Overall, wet 

months sustained higher WUA than dry months in the upper 

management section of the North Fork Shenandoah River.

The magnitude of habitat decline during natural dry 

periods can be seen in the time-series habitat values associated with extreme low flows recorded for the middle management section of the North Fork Shenandoah River (fig. 15). 

The maximum WUA is available at approximately 70 ft3/s for 

all four fish guilds (fig. 15). This is close to the median flow 

for July, August, and September. In the middle management 

section when flows are 70 ft3/s and decreasing, WUA for the 

riffle, fast-generalist, and pool-run guilds will also decrease. 

Sustained low-flows below this value in 1999 showed great 

habitat decline, and even some decline in pool-cover guild 

habitat area in August of 1999 when flows were less than 

10 ft3/s (fig. 15). 

In the middle management section, the fast-generalist, 

riffle, and pool-run guilds showed the greatest response to 

decreases in flow. The WUA for these three guilds was lowest 

during July, August, and September of 1964, and during June, 

July, and August of 1999 (fig. 15). The WUA for the fast-generalist guild decreased more than that for other guilds during 

low-flow periods. The WUA for riffle and pool-run guilds was 

more abundant than that for the fast-generalist guild, but the 

pattern of habitat decline in response to changes in flow was 

similar. The pool-cover guild WUA remained constant and did 

not show much response during past low-flow periods. During wet months (December-June), WUA remained constant. 

The WUA during wet months was frequently less than during 

dry months. Larger volumes of water in this section of the 

river may lead to habitat conditions that are too deep or fast 

for many fish, but is a normal habitat condition based upon 

seasonal patterns of flow. 

All four fish guilds within the lower management section were relatively unaffected by low flows shown in the 

time-series graphs (fig. 16). Based on the WUA curves (fig. 

13), this section should not show a great loss in habitat until 

flows are below the 90-percent exceedance value (87 ft3/s). 

Flows during the dry years examined dropped below this 

value infrequently (fig. 16). Because of the abundance of runs 

and pools in this section, and because pool-cover maximum 

WUA (fig. 13) is available over a wide range of flows, WUA 

in the lower management section will react slowly to changes 

in flow. Water quality during low flows is a concern, however. Lower flows and lower water depths may promote algal 

growth. During field data collection for a 1999 water-quality study of the North Fork Shenandoah River (Krstolic and 

Hayes, 2004), large filamentous mats of algae were observed 

in July. In conjunction with extreme low flows, dissolved oxygen levels can decline or fluctuate widely, as was observed in 

July 1999. As within the middle management section, during 

wet months (December-June), WUA in the lower management 

section was frequently less than during dry months. The WUA 

for the riffle and fast-generalist guilds varied much more 

widely during wet months than the WUA for the pool-run or 

pool-cover guilds. Seasonal patterns of habitat availability are 

representative of natural variations in flow.

Simulations of the zero water-withdrawal and double 

water-withdrawal scenarios were conducted for the entire 

period of record; however, the recent dry period of 1999 was 

selected to illustrate the pattern of WUA loss or gain represented by these simulations. The zero water-withdrawal scenario (adding back water withdrawals for June, July, August, 

and September) showed improvement in habitat availability 

for the fast-generalist guild species in the upper management 

section (fig. 17). All guilds showed improvements in WUA, 

but the fast-generalist guild showed the greatest response in 

the upper section. Water withdrawals are so minimal in the 

middle management section that the simulation showed little 

improvement. For the lower management section, reduced 

water use showed some improvement in pool-cover guild 

WUA (fig. 18). The zero-withdrawal scenario represents the 

upper limit for habitat availability during dry periods for all 

guilds. 

The double water-withdrawal scenario showed a total 

loss of fast-generalist guild WUA during July to mid-August 

of 1999 in the upper section (fig. 17). By subtracting 3.0 ft3/s 

from the historic discharge data, most of the simulated daily 

mean flows were equal to or less than 0.5 ft3/s during this time 

period. With simulated daily mean flows close to 0.0 ft3/s, 

the corresponding simulated WUA was equal to zero. This 

scenario demonstrates the scarcity of water in the upper section of the North Fork Shenandoah River. The double waterwithdrawal scenario for the middle section did not have much 

effect on simulated WUA. In the lower section, the double 
44 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River ����

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Figure 17. Weighted usable-habitat area for the fast-generalist fish guild under three different water-withdrawal scenarios in 1999 in the upper management section of the North Fork Shenandoah River, Virginia.
Instream Flow Modeling to Determine Fish Habitat Availability 45

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Figure 18. Weighted usable-habitat area for the pool-cover fish guild under three different water-withdrawal scenarios in 1999 in the lower management section of the North Fork Shenandoah River, Virginia.
46 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

water-withdrawal scenario showed a small decline in habitat 

availability for pool-cover guild species (fig. 18). Doubling of 

water withdrawals in this section of the North Fork Shenandoah River should have less effect on WUA than in the upper 

section. 

These two withdrawal scenarios show that an increase in 

the frequency of low flows below the flows that correspond to 

the maximum WUA would cause more habitat losses for riverine fish, but that conservation measures may help to lessen 

the effect on habitat during low-flow periods. Fish populations 

can recover from the effects of droughts over time and with 

low-flow periods occurring about every 10–30 years, the stress 

to the aquatic community likely would not cause permanent 

damage. Many of the flows discussed in this report represent 

natural flows that occur during frequently low-flow periods, 

yet rarely during normal years. However, if water withdrawals 

were to cause consistent, annual, drought-like conditions, fish 

populations could be affected year round and it is uncertain 

how well the aquatic community would recover. 

Summary and Conclusions

The objective of this study was to collect hydrologic, biologic, and habitat data for the North Fork Shenandoah River 

basin, focusing on availability of suitable habitat and maintenance of streamflows during low-flow periods. Study components included documentation of the mesohabitat distribution, 

analysis of historic streamflow data, collection of empirical 

river hydraulics data and fish community structure data, and 

development of fish habitat-suitability criteria and recreational-use suitability-criteria, all of which supported model 

development and time-series analysis of weighted usable area 

for the North Fork Shenandoah River. Since 1998 the U.S. 

Geological Survey has been working in cooperation with the 

Northern Shenandoah Valley Regional Commission on the 

present study and has partnered in data collection and analysis 

with Virginia Polytechnic Institute and State University. The 

North Fork Shenandoah River basin was the major focus of 

this study because the water supply is less than the other major 

tributary of the Shenandoah River, the South Fork Shenandoah 

River, and because 21 percent of the Shenandoah River basin 

population resides in the North Fork Shenandoah River basin. 

Maintaining health of the aquatic ecosystem, in concert with 

supplying water to a growing population and industry base, is 

of concern to local water-resoureces managers.

A modeling approach using empirical fish habitat requirements and physical stream habitat availability was selected. 

The RHABSIM model inputs include physical habitat data, 

microscale fish habitat-suitability criteria, and hydraulic data 

including water-surface elevation, depth, velocity, substrate, 

and discharge measurements. The large size of the basin 

(1,033 mi2) necessitated its division into three management 

sections for analysis purposes: the upper section, middle section, and lower section. The three sections are associated with 

the streamflow-gaging stations near the downstream end of 

each section: at Cootes Store, Va., at Mount Jackson, Va., and 

near Strasburg, Va. 

Despite past mill dams, some channelization for transportation, and the current water- withdrawal levels, streamflow 

of North Fork Shenandoah River varies with the seasons and 

weather, with high flows during winter and spring and lower 

flows during summer and fall. Within each management 

section, the historic streamflows were analyzed to determine 

the months with the lowest flows throughout the year. Flow 

statistics for the months of July, August, and September were 

used as a reference point to low-flow months, and the effect 

that flow reductions have on habitat during these months 

was assessed. Past low-flow years, when water was scarce 

throughout the basin, can be identified from the historic record 

when daily mean flows equal to or less than the 90-percent 

exceedance flow occurred an average of 50 percent of days 

during July, August, September, or October. The impact water 

withdrawals have on the system has not been assessed, but 

to this point (2004), the river is maintaining a fairly natural 

flow regime related to water availability, and during normal 

climatic years is largely unaffected by the withdrawals. This 

study focused on periods when streamflow is extremely low, 

when it may be difficult to achieve a balance between sustaining the aquatic community and using water to support the 

needs of people. 

Mesohabitat classification and mapping were completed 

to identify, describe, and quantify the mesohabitat types within 

the North Fork Shenandoah River. This inventory of mesohabitat along the entire river allowed RHABSIM model transects 

to be weighted to adequately represent mesohabitat types of 

the river. The general categories of habitat along the entire 

North Fork Shenandoah River include 14 percent riffle, 67.3 

percent run, and 18.7 percent pool. The percentages of rifle, 

run, and pool habitat are similar in each management section; 

however, mesohabitat unit length and substrate composition 

vary by section. In the upper section, the mesohabitat units are 

short, with many repeating riffle, run, riffle sequences. Particle-substrate riffles and runs are most common. The average 

length of an individual mesohabitat unit in the middle section 

is greater than the average length in the upper section, marking 

the transition between short, alternating sequences of riffles 

and runs, to longer stretches of riffles and runs. Few pools or 

backwater mesohabitat units were identified in the middle section. The lower section of the North Fork Shenandoah River is 

defined by long runs and artificial pools, which make up the 

longest individual mesohabitat units in the river. The extensive 

runs and artificial pools make the lower section slower to react 

to decreases in flow than the upstream sections. 

The mesohabitat classification assisted with the selection of hydraulic data-collection reaches and fish-sampling 

sites. Six hydraulic data-collection reaches and 36 transects 

were included in the study. Each river management section 

contained at least one reach, and the lower section contained 

four reaches. Hydraulic measurements included water depths, 

water velocities, transect discharges, and a best-estimate reach 
Summary and Conclusions 47

discharge during wadeable low-, medium-, and high-flow conditions in riffles, runs, and pools with a variety of substrates. 

Habitat-suitability criteria of fish are based on detailed fishcommunity sampling on the North Fork Shenandoah River, 

habitat observations, and analysis of collected data. To provide 

information that will describe the habitat utilized by multiple 

species and life stages of the fish community, fish species 

were grouped into guilds for development of habitat suitability 

criteria. 

Standard RHABSIM procedures were followed for 

each reach during calibration and simulation of water-surface elevations and velocities, and during habitat simulation. 

Habitat-discharge relations, or weighted usable-habitat area 

curves (WUA), were developed during habitat simulation. 

WUA curves were presented in the context of the normal flow 

regime for late summer and early fall. Understanding the availability of habitat during normal- and low-flow conditions on 

the North Fork Shenandoah River should aid water-resources 

managers in the creation of realistic management goals. The 

RHABSIM modeling results can be used to identify flow scenarios that limit or support WUA, and to identify which fish 

guilds are most affected in each river management section.

The upper management section has the least amount of 

flow, so it was expected that habitat within this reach would be 

most affected during low-flow periods. WUA is at a maximum 

at 42 ft3/s, a flow that approximately correlates to the 25-percent exceedance flow for July, August, and September. Habitat 

area is limited at and below the 90-percent exceedance flow 

(1.6 ft3/s). For most years, it is common in late summer and 

early fall for the river to sustain WUA less than the maximum 

WUA. 

 The middle management section is transitional between 

the headwaters in the upper section and the mouth in the 

lower section. It is the most diverse section of the North Fork 

Shenandoah River based on flow and mesohabitat, indicating 

that it may support fish within all guilds. The flows that sustain maximum WUA for all guilds are between 70 and 80 ft3

/s. 

These flows are within the normal range of flows for July, 

August, and September, indicating that the flows are available 50 percent of the time. WUA decreases with flows less 

than 75 ft3/s, and is very limited at and below the 99-percent 

exceedance flow for July, August, and September (8 ft3/s)

The lower section contains the longest and widest runs 

and pools. For the riffle, fast-generalist, and pool-run guilds, 

WUA is at a maximum at flows between 90 and 100 ft3/s. 

In the lower management section, the curve for the pool-run 

guild contains substantially greater area than the other three 

guild curves. For the pool-cover guild, WUA is at a maximum 

at 500 ft3/s. The WUA for the pool-cover guild is maintained 

at a constant level, with only slight decreases between 500 and 

65 ft3/s. WUA decreases and becomes limited at and below the 

99-percent exceedance flow for July, August, and September. 

The dynamic nature of WUA within the constructs of 

daily flow changes can be illustrated with time-series analysis. 

The habitat-discharge relation was overlain on the historic 

streamflow record, and two withdrawal scenarios were evaluated: zero water withdrawals and double water withdrawals. 

Flow is closely linked to habitat availability, and as the river 

enters a dry period, a reduction in flow generally corresponds 

to a reduction in WUA, and an increase in flow corresponds 

to an increase in WUA. During previous dry periods, timeseries analysis showed that habitat availability was limited for 

fast-generalist and pool-cover guilds in the upper management 

section; for riffle, fast-generalist, and pool-run guilds in the 

middle section; and for no guilds in the lower section. 

The zero water-withdrawal scenario (adding back water 

withdrawals for June, July, August, and September) showed 

increased WUA for fast-generalist guild species in the upper 

management section. In the upper section, all guilds showed 

improvements in WUA, but the fast-generalist guild showed 

the greatest response. Water withdrawals were so minimal in 

the middle management section that little improvement was 

shown. For the lower management section, there was some 

increase in WUA for the pool-cover guild WUA. 

The double water-withdrawal scenario (subtracting water 

withdrawals for June, July, August, and September) showed a 

total loss of fast-generalist guild WUA during July to midAugust of 1999 in the upper management section. Most of the 

simulated daily mean flows were equal to or less than 0.5 ft3/s 

during this time period, with the corresponding WUA close to 

zero. This scenario confirms the scarcity of water in the upper 

section of the North Fork Shenandoah River. Because of minimal reported water withdrawals, the double water-withdrawal 

scenario did not have much of an effect on simulated WUA 

in the middle section. The double water-withdrawal scenario 

showed a small decline in habitat availability for pool-cover 

guild species in the lower management section. Doubling of 

water withdrawals in this section of the North Fork Shenandoah River should have less of an effect on WUA than in the 

upper section.

These withdrawal scenarios show that an increase in the 

frequency of low flows below the flows that correspond to the 

maximum WUA would cause more habitat losses for riverine 

fish, but that water conservation measures may help to lessen 

the effect on habitat during low-flow periods. Decreases in 

flow during the high-flow season by water withdrawal and 

storage techniques likely would not cause more habitat losses 

for fish.

With the current flow regime, the model results indicate 

that habitat availability does not become very limited until the 

90-percent exceedance flows for July, August, and September 

are maintained for continuous periods; however, to support 

quality habitat requires the maintenance of streamflows within 

the normal range of flows for each management section. 

For the upper section, maximum WUA is available at flows 

close to 40 ft3/s. For July, August, and September the normal 

range of flows is between 4.4 and 40 ft3/s, and the 90-percent 

exceedance flow is 1.6 ft3/s. With current water withdrawals, 

during normal to wet years, flows naturally will remain within 

the range of 4.4 and 40 ft3/s. However, during dry years, or 

with increased water withdrawals, flows lower than the normal 

range of flows would likely be maintained for continuous peri-
48 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

ods. Maintaining flows lower than the normal range of flows 

each summer would consistently cause decreased WUA in this 

section. A reduction of flows to maintain the river at one given 

flow could cause a decline in the variety of habitats present 

and may contribute to water-quality problems. 

Seasonal instream conditions, current water withdrawals, 

and future water-use demands are all factors that can affect 

WUA and the extent to which a river can support a diverse fish 

community. Information on current and future water withdrawals and a better understanding of low-flow stream and 

habitat conditions, would be useful to water-resources managers in the development of a management plan for the North 

Fork Shenandoah River. 

Acknowledgments 

Many individuals and organizations contributed expertise, time, and support toward the completion of this study. 

The authors thank the Northern Shenandoah Valley Regional 

Commission (NSVRC) and its members, and all the members 

of the NSVRC Minimum Instream Flow Technical Advisory 

Committee for their time and support, as well as their interest in the health of the Shenandoah River basin; Dr. Donald J. 

Orth, and the staff of the Department of Fisheries and Wildlife 

Sciences, VPI, for their partnership in the design of the study, 

data collection, and evaluation; James A. Henriksen, Terry J. 

Waddle, and Ken D. Bovee from the USGS Ft. Collins MidContinental Ecological Science Center; and Thomas R. Payne 

from Thomas R. Payne and Associates for their support and 

suggestions throughout this study; and Patricia Maier and the 

Friends of the North Fork Shenandoah River for their assistance in contacting private landowners and obtaining permission for access to their land. The cooperation of public and 

private landowners who allowed access to the research sites is 

greatly appreciated.

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Appendix 1. RHABSIM Model-Calibration Data from the Hydraulic 

Data-Collection Reaches
52 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Appendix 1. RHABSIM model-calibration data from the hydraulic data-collection reaches.—Continued 

[WSL, water-surface elevation; ft, feet; ft3/s, cubic feet per second; verticals, number of measurement points along the transect; slope, average

water-surface slope for all discharges measured; SZF, stage zero flow; n.d., no data; ft/s, feet per second]

Transect

identification

Observed 

WSL1

(ft)

Simulated 

WSL

(ft)

Reach 

calibration 

discharge1

(ft3/s)

Modelcalculated 

discharge (ft3/s)

Verticals

Transect 

weighting 

factor

Slope1

(percent)

SZF1

(ft)

Average 

depth

(ft)

Wetted 

width

(ft)

Manning’s 

n3

Velocity 

mean

(ft/s)

Plains Mill

1

96.35 96.34 22.5 18

35 0.1 0.0011 94.24

1.65 96.03 0.48 0.14

97.03 97.05 109 106 2.24 100.65 .17 .48

97.11 97.10 121 n.d.2 2.31 101.17 .17 .52

97.50 97.54 264 n.d.2 2.63 103.98 .10 .97

97.81 97.77 379 357 2.87 106.63 .08 1.24

2

96.35 96.33 22.5 21

37 0 .0011 94.24

2.87 100.67 1.28 .08

97.03 96.95 109 n.d.2 3.39 105.92 .37 .30

96.92 97.03 92.5 77 3.31 105.08 .41 .27

97.46 97.52 264 264 3.73 108.49 .18 .65

97.81 97.74 379 n.d.2 4.01 110.56 .15 .85

3

97.05 97.05 22.5 22

43 1 .0046 95.92

0.60 81.12 .16 .46

97.73 97.71 109 n.d.2 1.05 107.25 .11 .97

97.75 97.77 121 139 1.06 108.14 .10 1.06

98.29 98.35 308 311 1.35 133.11 .07 1.71

98.55 98.50 379 n.d.2 1.57 136.28 .08 1.77

3A

97.25 97.24 22.5 13

44 1 .0003 95.92

1.18 100.40 .15 .19

97.92 97.95 109 105 1.64 118.02 .06 .56

98.03 98.01 121 n.d.2 1.74 119.09 .06 .58

98.60 98.62 308 295 2.22 124.29 .04 1.12

98.81 98.78 379 n.d.2 2.40 126.12 .04 1.25

3B

97.24 97.23 22.5 17

45 .2 .0003 95.92

3.41 122.62 1.08 .05

97.93 97.94 109 96 3.97 127.08 .30 .22

97.99 98.00 121 n.d.2 4.02 127.41 .28 .24

98.46 98.49 264 280 4.40 129.98 .15 .46

98.80 98.76 379 n.d.2 4.67 132.00 .12 .61

4

97.25 97.25 22.5 12

43 .5 .0003 95.92

3.32 135.49 1.15 .05

97.95 97.96 109 99 3.89 140.49 .32 .20

98.05 98.02 121 n.d.2 3.96 141.72 .30 .22

98.47 98.52 264 254 4.30 144.43 .16 .43

98.83 98.79 379 n.d.2 4.61 146.18 .13 .56

5

97.53 97.49 22.5 20

49 .1 .0002 96.47

0.57 111.31 .04 .35

98.05 98.12 109 n.d.2 0.85 153.53 .02 .84

98.14 98.18 121 134 0.94 154.39 .02 .83

98.61 98.63 264 n.d.2 1.37 158.61 .02 1.22

98.98 98.88 379 382 1.73 160.36 .02 1.37

6

97.62 97.57 22.5 24

43 .1 .0002 96.47

2.08 125.95 .40 .09

98.11 98.21 109 n.d.2 2.51 129.14 .12 .34

98.21 98.26 121 115 2.60 129.79 .11 .36

99.11 98.96 438 437 3.41 133.70 .05 .96

99.02 99.07 379 n.d.2 3.33 133.36 .06 .85
Appendix 53

Appendix 1. RHABSIM model-calibration data from the hydraulic data-collection reaches.—Continued 

[WSL, water-surface elevation; ft, feet; ft3/s, cubic feet per second; verticals, number of measurement points along the transect; slope, average

water-surface slope for all discharges measured; SZF, stage zero flow; n.d., no data; ft/s, feet per second]

Transect

identification

Observed 

WSL1

(ft)

Simulated 

WSL

(ft)

Reach 

calibration 

discharge1

(ft3/s)

Modelcalculated 

discharge (ft3/s)

Verticals

Transect 

weighting 

factor

Slope1

(percent)

SZF1

(ft)

Average 

depth

(ft)

Wetted 

width

(ft)

Manning’s 

n3

Velocity 

mean

(ft/s)

7

97.70 97.69 22.5 11

39 .5 .0002 96.47

0.71 64.62 0.03 .49

98.31 98.34 109 n.d.2 1.00 96.73 .02 1.13

98.44 98.39 121 129 1.07 102.43 .02 1.10

98.86 98.94 308 273 1.31 120.94 .01 1.94

99.15 99.09 379 n.d.2 1.59 122.17 .01 1.95

Spring Hollow

1

95.52 95.57 94.4 87

45 0.77 .0020 93.80

.98 70.25 .05 1.37

95.76 95.70 126 125 1.15 74.40 .05 1.47

96.46 96.46 432 407 1.63 87.60 .03 3.03

2

95.71 95.74 94.4 99

47 .5 .0048 94.30

.93 66.58 .06 1.52

95.92 95.89 126 128 1.07 71.62 .07 1.64

96.71 96.71 432 423 1.70 80.23 .05 3.17

3

95.97 95.99 94.4 96

46 .5 .0048 94.60

.76 75.63 .05 1.64

96.16 96.11 126 136 .92 78.00 .06 1.76

96.84 96.84 432 405 1.46 87.84 .04 3.37

4

96.13 96.15 94.4 108

44 .5 .0048 94.80

.78 74.85 .05 1.62

96.29 96.27 126 132 .87 80.99 .05 1.79

96.97 96.97 432 389 1.38 94.55 .04 3.31

5

96.45 96.45 94.4 100

50 .5 .0048 95.20

.90 99.43 .09 1.06

96.55 96.56 126 131 .99 100.29 .08 1.27

97.16 97.16 432 369 1.53 106.03 .05 2.66

Laurel Hill Farms

1

96.51 96.51 93.8 94

47 0.5 .0004 95.50

1.24 140.77 .07 0.54

96.66 96.66 120 121 1.38 142.27 .06 .61

97.64 97.64 400 405 2.27 149.42 .05 1.18

2

96.57 96.58 93.8 91

50 .5 .0004 95.50

.90 138.10 .04 .75

96.73 96.72 120 111 1.04 141.38 .04 .82

97.69 97.69 400 415 1.93 148.95 .03 1.39

3

96.78 96.78 93.8 98

49 1 .0004 95.50

.73 135.20 .03 .95

96.85 96.90 120 116 .79 136.34 .02 1.11

97.72 97.72 400 411 1.61 142.31 .02 1.75

4 97.04 97.03 93.8 109

46 .5 .0035 95.50

.96 119.47 .10 .82

97.10 97.13 120 135 1.01 120.67 .09 .98

97.72 97.72 400 376 1.49 134.88 .06 1.99

5 97.64 97.63 93.8 193

46 .5 .0246 95.50

1.02 144.50 0.37 .64

97.68 97.69 120 186 1.06 145.50 .31 .78

98.00 98.00 400 388 1.36 148.25 .14 1.98
54 Physical Habitat Classification and Instream Flow Modeling During Low-Flow Periods, North Fork Shenandoah River

Appendix 1. RHABSIM model-calibration data from the hydraulic data-collection reaches.—Continued 

[WSL, water-surface elevation; ft, feet; ft3/s, cubic feet per second; verticals, number of measurement points along the transect; slope, average

water-surface slope for all discharges measured; SZF, stage zero flow; n.d., no data; ft/s, feet per second]

Transect

identification

Observed 

WSL1

(ft)

Simulated 

WSL

(ft)

Reach 

calibration 

discharge1

(ft3/s)

Modelcalculated 

discharge (ft3/s)

Verticals

Transect 

weighting 

factor

Slope1

(percent)

SZF1

(ft)

Average 

depth

(ft)

Wetted 

width

(ft)

Manning’s 

n3

Velocity 

mean

(ft/s)

Route 648

1

89.50 89.53 83.34 n.d.2

36 0 .1008 88.11

0.76 135.25 0.48 0.81

89.51 89.55 86.98 133 .77 135.40 0.48 .83

89.93 89.76 136.00 144 1.16 140.40 0.62 .84

90.38 90.50 444.00 481 1.58 142.99 0.33 1.97

90.62 90.63 526.00 n.d.2 1.81 144.02 0.35 2.02

2

89.58 89.58 83.34 88

34 1 .0142 88.11

1.44 140.18 0.55 .41

89.60 89.60 86.98 n.d.2 1.46 140.33 0.54 .42

90.00 90.00 136.00 135 1.82 143.34 0.51 .52

90.48 90.48 444.00 n.d.2 2.28 144.86 0.23 1.34

90.69 90.69 526.00 523 2.49 145.33 0.22 1.45

3

89.59 89.59 83.34 112

35 1 .0142 88.11

2.11 131.79 0.97 .30

89.60 89.61 86.98 n.d.2 2.12 131.83 0.94 .31

90.01 90.01 136.00 138 2.50 133.58 0.80 .41

90.50 90.55 444.00 n.d.2 2.95 135.68 0.33 1.11

90.76 90.77 526.00 617 3.19 136.79 0.32 1.21

4

89.61 89.59 83.34 n.d.2

32 0 .0142 88.11

2.69 119.11 1.31 .26

89.62 89.61 86.98 n.d.2 2.70 119.17 1.27 .27

90.04 90.02 136.00 126 3.06 121.76 1.02 .37

90.60 90.59 444.00 n.d.2 3.52 125.70 0.41 1.00

90.81 90.82 526.00 n.d.2 3.67 127.62 0.37 1.12

5

89.61 89.60 83.34 n.d.2

36 1 .0142 88.11

1.96 134.59 0.88 .32

89.62 89.62 86.98 106 1.97 134.74 0.85 .33

90.05 90.02 136.00 128 2.35 137.82 0.74 .42

90.66 90.61 444.00 n.d.2 2.89 141.68 0.33 1.08

90.82 90.84 526.00 544 3.03 142.69 0.30 1.22

6

89.62 89.60 83.34 98

37 .2 .0171 88.11

2.52 123.88 1.35 .27

89.64 89.62 86.98 n.d.2 2.53 124.40 1.31 .28

90.07 90.03 136.00 124 2.76 134.32 1.04 .37

90.66 90.64 444.00 469 3.17 142.97 0.43 .98

90.89 90.87 526.00 n.d.2 3.36 144.51 0.40 1.08

7

89.65 89.60 83.34 92

37 .8 .0171 88.11

1.58 137.59 0.69 .38

89.64 89.63 86.98 n.d.2 1.57 137.50 0.65 .40

90.07 90.04 136.00 138 1.95 141.25 0.62 .49

90.66 90.68 444.00 n.d.2 2.49 144.55 0.29 1.23

90.93 90.91 526.00 573 2.74 145.87 0.29 1.32

8

89.66 89.61 83.34 85

39 .5 .0171 88.11

2.21 147.14 1.29 .26

89.66 89.63 86.98 n.d.2 2.21 147.14 1.23 .27

90.09 90.05 136.00 129 2.57 151.31 1.04 .35

90.69 90.73 444.00 439 3.10 155.09 0.45 .92

90.93 90.97 526.00 n.d.2 3.31 156.44 0.43 1.02
Appendix 55

Appendix 1. RHABSIM model-calibration data from the hydraulic data-collection reaches.—Continued 

[WSL, water-surface elevation; ft, feet; ft3/s, cubic feet per second; verticals, number of measurement points along the transect; slope, average

water-surface slope for all discharges measured; SZF, stage zero flow; n.d., no data; ft/s, feet per second]

Transect

identification

Observed 

WSL1

(ft)

Simulated 

WSL

(ft)

Reach 

calibration 

discharge1

(ft3/s)

Modelcalculated 

discharge (ft3/s)

Verticals

Transect 

weighting 

factor

Slope1

(percent)

SZF1

(ft)

Average 

depth

(ft)

Wetted 

width

(ft)

Manning’s 

n3

Velocity 

mean

(ft/s)

Posey Hollow

1

91.35 91.39 122 104

43 0 .0006 89.7

0s.93 180.65 0.05 0.73

91.77 91.66 219 239 1.33 184.55 .05 .89

92.23 92.30 666 525 1.78 185.83 .03 2.01

2

91.38 91.41 122 174

42 0.1 .0006 89.7

2.22 170.24 .19 .32

91.84 91.83 219 229 2.65 172.66 .14 .48

92.32 92.33 666 761 3.10 174.21 .06 1.23

3

91.38 91.42 122 127

41 0.5 .0006 89.7

2.35 171.12 .20 .30

91.85 91.85 219 220 2.77 174.64 .15 .45

92.34 92.36 666 671 3.23 176.03 .07 1.17

4

91.47 91.47 122 127

41 0.8 .0006 89.7

1.72 171.08 .12 .41

91.93 91.90 219 220 2.15 173.57 .10 .59

92.39 92.42 666 738 2.59 175.22 .05 1.47

5

91.53 91.48 122 142

44 0.2 .0009 89.7

2.87 184.53 .39 .23

91.98 91.91 219 203 3.26 188.04 .28 .36

95.50 92.45 666 812 3.66 188.96 .11 .96

Winchester Dam

1

95.39 95.37 195 130

41 0.5 .0012 94.00

3.81 173.18 .43 0.30

95.40 95.41 218 178 3.82 173.23 .39 .33

95.88 95.90 654 752 4.24 175.62 .16 .88

95.92 95.94 696 n.d.2 4.28 175.82 .15 .93

96.39 96.36 1430 1436 4.69 178.16 .09 1.71

2

95.40 95.39 195 183

42 .5 .0012 94.00

3.70 169.25 .40 .31

95.41 95.40 218 168 3.71 169.27 .36 .35

95.88 95.88 654 n.d.2 4.15 170.44 .15 .92

95.94 95.92 696 802 4.21 170.59 .14 .97

96.40 96.40 1430 1404 4.64 171.73 .08 1.79

3

95.41 95.39 195 120

42 .5 .0012 94.00

4.30 168.31 .51 .27

95.42 95.40 218 220 4.31 168.34 .46 .30

95.89 95.89 654 n.d.2 4.75 169.52 .18 .81

95.95 95.93 696 773 4.81 169.66 .17 .85

96.40 96.42 1430 1379 5.23 170.70 .10 1.60

1 Value calculated from field measurements.

 2 No velocity dataset collected for this water-surface elevation.

 3 Manning’s n calculated with average slope for the reach where n = 1.486/V * R2/3 * S1/2 (n, coefficient of roughness; V, mean channel velocity;

R, hydraulic radius, in this case, average depth; S, slope)