Simulation of Flow and Sediment Mobility Using a

Multidimensional Flow Model for the White Sturgeon

Critical-Habitat Reach, Kootenai River near

Bonners Ferry, Idaho 

Scientific Investigations Report 2005–5230

Prepared in cooperation with the 

Kootenai Tribe of Idaho and 

Bonneville Power Administration

U.S. Department of the Interior

U.S. Geological Survey

55,000

44,000

33,000

22,000

11,000

0

3,000

2,400

1,800

1,200

600

0

A. Pre-Libby Dam era, 1966-71

Streamflow

Suspended-sediment load
Cover: Photograph of Kootenai River at Bonners Ferry, photograph taken near river kilometer 245. 

View facing upstream with bedrock outcropping in the foreground and the Union Pacific Railroad 

bridge in the background. (Photograph by Gary Barton, U.S. Geological Survey, April 2005.)
Simulation of Flow and Sediment Mobility 

Using a Multidimensional Flow Model for the 

White Sturgeon Critical-Habitat Reach, 

Kootenai River near Bonners Ferry, Idaho

By Gary J. Barton, Richard R. McDonald, Jonathan M. Nelson, and

Randal L. Dinehart

Prepared in cooperation with the Kootenai Tribe of Idaho and

Bonneville Power Administration

Scientific Investigations Report 2005-5230

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: 2005

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

Box 25286, Denver Federal Center

Denver, CO 80225

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Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Barton, G.J., McDonald, R.R., Nelson, J.M., and Dinehart, R.L., 2005, Simulation of flow and sediment mobility using 

a multidimensional flow model for the white sturgeon critical-habitat reach, Kootenai River near Bonners Ferry, Idaho: 

U.S. Geological Survey Scientific Investigations Report 2005-5230, 54 p.
iii

Contents

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

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

Purpose and Scope ................................................................................. 2

Acknowledgments ................................................................................. 2

Description of the Study Reach ........................................................................ 5

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 7

Streamflow .......................................................................................... 7

Composition of Channel Substrate ............................................................... 10

Sediment-Transport Regime ..................................................................... 13

River Channel Geometry ........................................................................... 14

Bathymetry and Streambank Topography ................................................ 14

Dunes and Other Bedforms .................................................................. 16

River Channel Degradation and Aggradation ............................................. 16

Construction of the Multidimensional Flow Model ................................................... 20

Computational Grid and Bathymetric Interpolation ............................................. 20

Streamflow Velocity at the Upstream Model Boundary ....................................... 22

Water-Surface Elevation at the Downstream Model Boundary .............................. 22

Model Calibration ................................................................................. 22

Model Boundary Conditions for Calibration Runs ....................................... 25

Drag Coefficient .............................................................................. 25

Results.......................................................................................... 25

Model Validation .................................................................................... 26

Model Sensitivity Analysis ........................................................................ 31

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach ...... 34

Water-Surface Elevation Profiles and Free-Flowing and Backwater Streamflow ......... 35

River Depth .......................................................................................... 36

Streamflow Velocity .............................................................................. 37

Sediment Mobility ................................................................................. 46

Model Limitations ....................................................................................... 49

Summary ................................................................................................... 49

References Cited.......................................................................................... 51

Appendix A. Processing Acoustic Doppler Current Profiler Data ................................. 53
iv

Figures

Figure 1. Map showing location of study area, near Bonners Ferry, Idaho, and

selected streamflow-gaging stations and dams in the Kootenai River

drainage basin, Idaho, Montana, and British Columbia, Canada ..................... 3

Figure 2. Map showing location of the white sturgeon critical-habitat reach and

upstream and downstream boundaries for the multidimensional flow model

on the Kootenai River near Bonners Ferry, Idaho ....................................... 4

Figure 3. Graph showing location and number of white sturgeon spawning events

and spawning events per unit effort on the Kootenai River near Bonners

Ferry, Idaho, 1994 to 2001 .................................................................. 6

Figure 4. Graphs showing annual median daily streamflow and suspended-sediment

load for the pre-Libby Dam era (1966–71) and Libby Dam era (1973–82) and

annual streamflow and suspended-sediment load, 1966–82, Kootenai River

at Copeland, Idaho........................................................................... 8

Figure 5. Graphs showing streamflow, water-surface elevation, and water-surface

slope of the white sturgeon critical-habitat reach of the Kootenai River,

Bonners Ferry, Idaho, and water-surface elevation of Kootenay Lake,

1965–2003 .................................................................................... 9

Figure 6. Map showing location of sediment core sites sampled in 2000 and 2004 on

the white sturgeon critical-habitat reach of the Kootenai River near Bonners

Ferry, Idaho ................................................................................. 11

Figure 7. Map showing location of streambed-sediment sampling sites on the white

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry,

Idaho .......................................................................................... 12

Figure 8. Graph showing particle-size distribution for streambed sediment samples

taken between river kilometers 228.4 and 245.8 on the white sturgeon

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho ............ 13

Figure 9. Graph showing daily mean flow and water-surface elevation for the white

sturgeon critical-habitat reach of Kootenai River near Bonners Ferry, Idaho,

2002 and 2003................................................................................. 15

Figure 10. Map showing location of acoustic Doppler current profiler cross sections

and longitudinal profiles for monitoring riverbed stability and bedforms on

the white sturgeon critical-habitat reach of the Kootenai River near Bonners

Ferry, Idaho ................................................................................. 17

Figure 11. Graphs showing changes in bedforms along longitudinal profiles measured

with an acoustic Doppler current profiler in the white sturgeon

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho,

2002 .......................................................................................... 18

Figure 12. Graphs showing aggradation and degradation of streambed at five cross

sections of the white sturgeon critical-habitat reach of the Kootenai River

near Bonners Ferry, Idaho, 2002 ......................................................... 19

Figure 13. Aerial photographs showing nodes forming an approximately

5.0-by-5.0-meter grid in the multidimensional flow model at the upstream

end of Shorty Island in the white sturgeon critical-habitat reach of the

Kootenai River near Bonners Ferry, Idaho................................................ 21

Figure 14. Graph showing streamflow-velocity measurements at the upstream model

boundary on the white sturgeon critical-habitat reach of the Kootenai River

at Bonners Ferry, Idaho, June 1996 and April 2002 .................................... 23
Figure 15. Graph showing drag and lateral eddy-viscosity coefficients for the calibrated

multidimensional flow model of the white sturgeon critical-habitat reach of

the Kootenai River near Bonners Ferry, Idaho .......................................... 26

Figure 16. Map showing location of acoustic Doppler current profiler cross sections for

validating the multidimensional flow model for the white sturgeon

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho ............ 27

Figure 17. Cross sections showing measured cross sections of vertically averaged

velocities and corresponding simulated velocities on the white sturgeon

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, 

for a steady flow that averaged 538 cubic meters per second on 

August 12–14, 2003 ........................................................................ 28

Figure 18. Graph showing functional dependence of the drag coefficient on depth, used

to improve simulated vertically averaged velocity at cross section 2313 on the

Kootenai River near Bonners Ferry, Idaho................................................ 30

Figure 19. Cross sections showing measured vertically averaged velocity and simulated

vertical velocity based on a constant drag coefficient and variable drag

coefficient for cross-section 2313 on the white sturgeon critical-habitat

reach of the Kootenai River near Bonners Ferry, Idaho, for a steady flow that

averaged 538 cubic meters per second on August 12–14, 2003 ........................... 30

Figure 20. Cross sections showing measured and simulated vertical profiles of

downstream velocity and cross-stream velocity at section 2370 on the white

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, 

Idaho, for a steady flow that averaged 538 cubic meters per second on 

August 12–14, 2003 ........................................................................... 32

Figure 21. Graph showing simulated average water-surface elevation for five

streamflows at cross sections positioned every 100 meters along the white

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry,

Idaho, and spawning event locations ................................................... 36

Figure 22. Graph showing simulated average and maximum depth for five streamflows

at cross sections positioned every 100 meters along the white sturgeon

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and

spawning event locations .................................................................. 37

Figure 23. Graph showing simulated average and maximum velocity for five

streamflows at cross sections positioned every 100 meters along the white

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry,

Idaho, and spawning event locations ................................................... 38

Figure 24. Graph showing standard deviation of simulated velocity for five streamflows

at cross sections positioned every 100 meters along the white sturgeon

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and

spawning event locations .................................................................. 39

Figure 25. Aerial photographs showing distribution of simulated velocity for five

streamflows in the white sturgeon critical-habitat reach of the Kootenai River

near Bonners Ferry, Idaho.................................................................. 40

Figure 26. Graph showing simulated sediment mobility and critical shear stress for five

streamflows at cross sections positioned every 100 meters along the white

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry,

Idaho, and spawning event locations ................................................... 48

Figures—Continued
vi

Conversion Factors and Datums

Conversion Factors

Multiply By To obtain

centimeter (cm) 0.3937 inch

cubic meter per day (m3/d) 35.31 cubic foot per day

cubic meter per day (m3/d) 264.2 gallon per day

cubic meter per second (m3/s) 70.07 acre-foot per day

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

kilometer (km) 0.6214 mile

meter (m) 3.281 foot

meter per second (m/s) 3.281 foot per second

metric ton per day (mt/d) 1.102 ton per day

millimeter (mm) 0.03937 inch

square kilometer (km2) 247.1 acre

square kilometer (km2) 0.3861 square mile

square meter (m2) 0.0002471 acre

Pressure: 1 Pascal (Pa) = 1N/m2 = 6.895 kPa.

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

 °F=(1.8x°C)+32.

Datums

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

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83), 

Idaho Transverse Mercator—North American Datum 1983/1998 Idaho West, in meters.

Tables

Table 1. Amplitude and wavelength of dune bedforms in the white sturgeon

critical-habitat reach of the Kootenai River, near Bonners Ferry, Idaho ............ 16

Table 2. Calibration summary for the multidimensional hydraulic flow model for the

white sturgeon critical-habitat reach of the Kootenai River, near Bonners

Ferry, Idaho ................................................................................. 24

Table 3. Sensitivity analysis and results of the multidimensional flow model for the

white sturgeon critical-habitat reach of the Kootenai River near Bonners

Ferry, Idaho, for five streamflows ......................................................... 34

Table 4. Upstream and downstream boundary conditions in the multidimensional

flow model for the white sturgeon critical-habitat reach of the Kootenai

River near Bonners Ferry, Idaho ......................................................... 35

Table 5. Sediment grade scale and critical shear stress for determining approximate

condition for sediment mobility at 20 degrees Celsius ................................. 46
Simulation of Flow and Sediment Mobility Using a Multidimensional 

Flow Model for the White Sturgeon Critical-Habitat Reach, 

Kootenai River near Bonners Ferry, Idaho

By Gary J. Barton, Richard R. McDonald, Jonathan M. Nelson, and Randal L. Dinehart

Abstract

In 1994, the Kootenai River white sturgeon (Acipenser 

transmontanus) was listed as an Endangered Species as a 

direct result of two related observations. First, biologists 

observed that the white sturgeon population in the Kootenai 

River was declining. Second, they observed a decline in 

recruitment of juvenile sturgeon beginning in the 1950s with 

an almost total absence of recruitment since 1974, following 

the closure of Libby Dam in 1972. This second observation 

was attributed to changes in spawning and (or) rearing habitat 

resulting from alterations in the physical habitat, including 

flow regime, sediment-transport regime, and bed morphology 

of the river. The Kootenai River White Sturgeon Recovery 

Team was established to find and implement ways to improve 

spawning and rearing habitat used by white sturgeon. They 

identified the need to develop and apply a multidimensional 

flow model to certain reaches of the river to quantify physical 

habitat in a spatially distributed manner. The U.S. Geological 

Survey has addressed these needs by developing, calibrating, 

and validating a multidimensional flow model used to simulate 

streamflow and sediment mobility in the white sturgeon 

critical-habitat reach of the Kootenai River. This report 

describes the model and limitations, presents the results of 

a few simple simulations, and demonstrates how the model 

can be used to link physical characteristics of streamflow to 

biological or other habitat data. This study was conducted in 

cooperation with the Kootenai Tribe of Idaho along a 

23-kilometer reach of the Kootenai River, including the white 

sturgeon spawning reach near Bonners Ferry, Idaho that is 

about 108 to 131 kilometers below Libby Dam. 

U.S. Geological Survey’s MultiDimensional SurfaceWater Modeling System was used to construct a flow model 

for the critical-habitat reach of the Kootenai River white 

sturgeon, between river kilometers 228.4 and 245.9. Given 

streamflow, bed roughness, and downstream water-surface 

elevation, the model computes the velocity field, water-surface 

elevations, and boundary shear stress throughout the modeled 

reach. The 17.5 kilometer model reach was subdivided into 

two segments on the basis of predominant grain size: a 

straight reach with a sand, gravel, and cobble substrate located 

between the upstream model boundary at river kilometer 245.9 

and the upstream end of Ambush Rock at river kilometer 

244.6, and a meandering reach with a predominately sand 

substrate located between upstream end of Ambush Rock and 

the downstream model boundary at river kilometer 228.4. 

Model cell size in the x and y (horizontal) dimensions is 

5 meters by 5 meters along the computational grid centerline 

with 15 nodes in the z (vertical) dimension. The model was 

calibrated to historical streamflows evenly distributed between 

141.6 and 2,548.9 cubic meters per second. The model was 

validated by comparing simulated velocities with velocities 

measured at 15 cross sections during steady streamflow. These 

15 cross sections were each measured multiple (7–13) times to 

obtain velocities suitable for comparison to the model results. 

Comparison of modeled and measured velocities suggests that 

the model does a good job of reproducing flow patterns in the 

river, although some discrepancies were noted.

The model was used to simulate water-surface elevation, 

depth, velocity, bed shear stress, and sediment mobility 

for Kootenai River streamflows of 170, 566, 1,130, 1,700, 

and 2,270 cubic meters per second (6,000, 20,000, 40,000, 

60,000, and 80,000 cubic feet per second). The three lowest 

streamflow simulations represent a range of typical river 

conditions before and since the construction of Libby Dam, 

and the highest streamflow simulation (2,270 cubic meters 

per second) is approximately equal to the annual median peak 

streamflow prior to emplacement of Libby Dam in 1972. 

Streamflow greater than 566 cubic meters per second were 

incrementally increased by 570 cubic meters per second. 

For each of the five streamflow simulations, the average, 

maximum, and standard deviation of water-surface elevation, 

depth, velocity, and sediment mobility were quantified at 

174 cross sections of the river channel (positioned every 

100 meters along the length of the model reach). Simulated 

conditions along the critical-habitat reach were compared with 

locations of white sturgeon spawning events, based on the 

number of spawning events per unit of effort during 1994-

2001, to demonstrate how the model can be used to relate 

observed spawning or other observed habitat-related behavior 

to local physical characteristics of the river. With further 

applications focused on specific spawning or rearing habitat 

questions, the model potentially is a useful tool for relating 

river flows to quantitative assessments of habitat quality and 

quantity.
Introduction

Many local, State, and Federal agencies are concerned 

about the declining population of white sturgeon (Acipenser 

transmontanus) in the Kootenai River in Idaho (fig. 1). 

In 1994, Kootenai River white sturgeon was listed as 

an Endangered Species, and fishing for this species was 

prohibited. The decrease in the white sturgeon population 

apparently is driven by an overall decline in spawning success, 

as reflected by the presence of few juvenile sturgeon (U.S. 

Fish and Wildlife Service, 1999). Observations suggest that 

a decline in recruitment of white sturgeon began in the 1950s 

and the last successful recruitment was in 1974 (Paragamian 

and others, 2005). (Recruitment refers a spawning event that 

produces juvenile fish that survive to create a new year-class 

of fish in sufficient numbers to maintain fish population.) 

Lack of Kootenai River white sturgeon recruitment has 

been attributed, at least in part, to changes in the natural 

streamflow regime of the Kootenai River after emplacement 

of Libby Dam, near Libby, Montana, in 1972 (U.S. Fish and 

Wildlife Service, 1999). The reservoir upstream of the dam, 

Lake Koocanusa, completely filled in 1974. Accompanying 

changes in the flow hydrograph, sediment supply, and bed 

morphology downstream of the dam are hypothesized to have 

adversely affected distribution of channel substrate and other 

elements of sturgeon spawning habitat near Bonners Ferry, 

Idaho (fig. 2; Collier and others, 1996). Other changes in the 

Kootenai River that could have affected sturgeon recruitment 

include the construction of dikes on natural levees, changes in 

backwater conditions near Bonners Ferry caused by changes in 

the level of Kootenay Lake, loss of wetlands in the river valley, 

reduction of the river’s nutrient load, and fishing. 

The Kootenai River White Sturgeon Recovery Team, 

composed of scientists and engineers from the Kootenai Tribe 

of Idaho (KTOI), Idaho Department of Fish and Game, and 

several local, State, Federal, and Canadian agencies, is trying 

to reestablish recruitment of white sturgeon by developing 

a better understanding of the physical factors affecting 

quality and quantity of spawning and rearing habitat, and by 

using that understanding to design and implement ways to 

improve that habitat. In view of these goals, the Recovery 

Team has a need to relate observed biological behavior (for 

example, spawning) to local physical characteristics of the 

river. Establishing these relations requires riverine-flow and 

sediment-transport models that provide spatially distributed 

(at a point) simulation of physical characteristics of the river. 

In response to this need, the U.S. Geological Survey (USGS), 

in cooperation with the KTOI, during a 4-year study collected 

hydraulic, topographic, and sediment data that were used to 

develop a multidimensional flow model and a 1-dimensional 

sediment-transport model of the white sturgeon critical-habitat 

reach near Bonners Ferry, Idaho (fig. 2). These models can 

be used as tools to quantify the local characteristics of the 

flow and sediment transport and can also serve to assess 

the feasibility of various habitat-enhancement scenarios to 

re-establish recruitment of white sturgeon. For example, 

modeling assessments might be used to (1) determine whether 

a proposed spawning substrate structure will be susceptible 

to erosion or deposition, (2) test that streamflow velocity at 

a proposed spawning-substrate structure will be high enough 

to minimize egg predation for a given flow, or (3) identify 

potential hydraulic cues used by white sturgeon to initiate 

spawning. Although both models simulate water-surface 

elevation, depth, velocity, shear stress, and sediment-transport 

characteristics, the 1-dimensional model provides only a single 

cross-sectionally averaged value at each river cross section, 

whereas the multidimensional model provides those values 

at every location in the river. The 1-dimensional model is 

described in detail by Berenbrock and Bennett (2005).

Purpose and Scope

The purposes of this report are to (1) discuss construction, 

calibration, and validation of the multidimensional flow model 

used to simulate streamflow and sediment mobility in the 

white sturgeon critical-habitat reach of the Kootenai River; (2) 

present results of a few simple simulations and demonstrate 

how the model can be used to link physical characteristics of 

streamflow to biological or other habitat data; and (3) discuss 

limitations of the model. Data needed for the study included 

general channel characteristics, channel topography and 

bathymetry, particle grain-size distributions making up the 

channel bed, bedform presence and geometry, water-surface 

elevations, and streamflow velocity.

Acknowledgments

The authors thank the people of the Kootenai River 

Valley in Idaho, Montana, and British Columbia who provided 

access to the Kootenai River for surveying. Sue Ireland of 

the KTOI provided storage facilities for USGS boats and 

equipment. Vaughn Paragamian, Diane Wakkinnen, and Peter 

Rust of Idaho Department of Fish and Game (IDFG) provided 

white sturgeon spawning location and egg location data. The 

authors also appreciate that the KTOI collected suspendedsediment samples from the Kootenai River at Bonners Ferry 

and provided logistical support for field work. Rick Backsen, 

John Gralow, and Russ Christensen of USGS in Post Falls, 

Idaho, Edward Moran of USGS in Anchorage, Alaska, and 

Charles Berenbrock of USGS in Boise, Idaho, worked long 

hours collecting data on the Kootenai River for this project. 

Sandra Ball of USGS in Post Falls, Idaho, helped with many 

logistic issues. Kimberly Mueller, student, and Theresa 

Olsen, with USGS in Tacoma, Washington, entered survey 

control field measurements into the National Geodetic Survey 

database and provided geographical information systems 

support. Mary Donato of USGS in Boise, Idaho, provided a 

graphical illustration of IDFG’s white sturgeon spawning and 

egg location data. 

 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 1. Location of study area, near Bonners Ferry, Idaho, and selected streamflow-gaging stations and dams in the Kootenai River drainage basin, Idaho, Montana, and 

British Columbia, Canada.

ID91Z00l_fig01

Creek Lake

Kootenay

River

Moyie River

River

Yaak

River

Kootenai

River

Kootenay

Lake

Koocanusa

River Mary St.

Fisher

West

Arm

Kootenay Lake

Columbia

River

Columbia

Lake

River

Tobacco

Slocan

Lake

River

Slocan

River

Libby

Dam

Lake

Creek

Dam

Kootenai

Falls

Dam

Moyie

Dam

Corra

Lynn

Dam

Bonners

Ferry

Shorty

 Island

Troy

Libby

Creston

Porthill

Nelson

Castlegar

Crossport

Moyie Springs

Queens

Bay

Proctor

Bonnington Falls

Grohman

Narrows

Copeland

Kimberley

Cranbrook

00

40 20 60 80 KILOMETERS

20 40 MILES

Base from U.S. Geological Surveydigital data, 1:100,000, 1980Albers Equal-Area projectionStandard parallels 43° 30', 47° 30',and -114° 00', 41° 45'No false easting or false northing

117° 116° 115°

118°

49°

50°

BRITISH

COLUMBIA

IDAHO

MONTANA

CANADA

UNITED STATES

PURCELL

TRENCH

PURCELL

MOUNTAINS

SELKIRK

MOUNTAINS

CABINET

MOUNTAINS

R O C K Y

M O U N T A I N S

S A L I S H

M O U N T A I N S

12318500

12304500

12301933 12302055

12322000

O8NH067 or

12322500

O8NH064

O8NH064

12321500

12309500

12310100

12314000

EXPLANATION

STUDY AREA SHOWN IN FIGURE 2U.S. GEOLOGICAL SURVEY  GAGING STATION AND NO.WEST KOOTENAY POWER AND LIGHT GAGING STATION

12318500

CANADA

UNITED STATES

Kootenai River

Drainage Basin

Introduction 
ID91Z00_fig02

2

95

95

2

Burlington

Northern

Santa Fe 

Railroad

Union

Pacific

Railroad

Pacific

Union

Railroad

BNSF Railroad

River

IDAHO 

Bonners

Ferry

Deep

Creek 

Myrtle Creek 

Shorty

Island

Lost Creek 

Ball

Creek 

Ambush

Rock

Mission

Hill

S E L K I R K R A N G E 

Kootenai

K O O T E N A I F L A T S 

K O O T

E N A I F L A T S 

Downstream

boundary for 

multidimensional

model

Upstream

boundary for

multidimensional

model

BRAIDED REACH

STRAIGHT

REACH

MEANDER

REACH

12310100

12309500

12314000 Kilometer 225 

Kilometer 230 

Kilometer 235 

Kilometer 240 

Kilometer 245

Kilometer 250 

116° 25' 116° 20'

48°

45'

48°

40'

EXPLANATION

AREA ABOVE FLOOD PLAIN

WHITE STURGEON CRITICAL-HABITAT REACH —

 River kilometer 228 to 246

RIVER KILOMETER

U.S. GEOLOGICAL SURVEY 

 GAGING STATION AND NO.

Kilometer 235

12309500

+

Base from U.S. Geological Survey digital data, 1:100,000, 1983

Universal Transverse Mercator projection, Zone 13

0

0 1 2 MILES

1 2 3 4 KILOMETERS 

Figure 2. Location of the white sturgeon critical-habitat reach and upstream and downstream boundaries for the 

multidimensional flow model on the Kootenai River near Bonners Ferry, Idaho. 

 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Description of the Study Reach

Kootenai River begins in British Columbia, Canada, 

flows through Montana and Idaho, and then turns northwest 

back into British Columbia (fig. 1). Kootenai River is referred 

to as the Kootenay River in British Columbia. For the purpose 

of this report and as a matter of convenience, the United 

States spelling (Kootenai) will be used when referring to 

the river and the Canadian spelling (Kootenay) will be used 

when referring to the lake, which is located entirely within 

British Columbia, Canada. The drainage basin is within the 

Northern Rocky Mountains physiographic province, which 

is characterized by north- to northwest-trending mountain 

ranges. The Rocky Mountains form much of the eastern basin 

boundary, the Selkirk Mountains form the western basin 

boundary, and the Cabinet Mountains form the southern basin 

boundary. Kootenai River is 721 kilometers (km) long and 

drains an area of 45,584 square kilometers (km2). The study 

area is a reach of Kootenai River near Bonners Ferry, Idaho, 

which comprises the spawning habitat for the Kootenai River 

population of endangered white sturgeon (figs. 1 and 2). The 

designated critical habitat for white sturgeon ranges from 

river kilometer (RKM) 225.0 to 246.7 (fig. 2; U.S. Fish and 

Wildlife Service, 2000). Litigation may result in extending the 

critical-habitat reach further upstream (Bob Hallock, U.S. Fish 

and Wildlife Service, oral commun., 2006).

The altitude at the headwaters of the river in British 

Columbia is 3,618 meters (m). Kootenai Falls, where the river 

loses 61 m of altitude over a distance of about 100 m, is the 

only waterfall between Libby Dam and Kootenay Lake and is 

46 km downstream of the dam. Kootenai Falls forms a natural 

fish-migration barrier. At Bonners Ferry, 111 km downstream 

of Libby Dam near the upstream end of the white sturgeon 

critical habitat, Kootenai River flows westward into a nearly 

straight, northwest-trending, 480-km-long trough known as the 

Purcell Trench. The Purcell Trench is flanked by the Selkirk 

Mountains on the west and by the Purcell Mountains on the 

east. Here, the river meanders northwest through the broad, 

flat bottomlands referred to as Kootenai Flats (figs. 1 and 

2) for about 80 km to Kootenay Lake near Creston, British 

Columbia. Kootenai River then flows from the lower end of 

the West Arm of Kootenay Lake for about 32 km and empties 

into the Columbia River at Castlegar, British Columbia. 

Bonnington Falls, with its series of four dams, including Corra 

Lynn Dam, isolates white sturgeon from other populations 

of fish in the Columbia River Basin. This disconnection 

apparently is not recent; a natural barrier at Bonnington 

Falls has isolated the Kootenai River white sturgeon for 

approximately 10,000 years (Northcote, 1973). 

Snyder and Minshall (1996) classified three geomorphic 

reaches in the Kootenai River between Libby Dam and 

Kootenay Lake: a canyon reach, a braided reach, and a 

meander reach. The canyon reach extends from Libby Dam 

to 2 km downstream of the mouth of Moyie River. Here, the 

valley broadens and the river forms a low-gradient braided 

reach as it courses over gravel and cobbles. This braided 

reach extends downstream into the study area to a bedrock 

constriction near the U.S. Highway 95 Bridge over Kootenai 

River at Bonners Ferry. A straight reach between RKM 245.9 

and 244.5 forms a transition zone between the meandering 

reach and the braided reach. This straight reach was first 

described by Tetra Tech, Inc. (2003). The meander reach is 

sandy and extends from RKM 244.5, about 4.5 km upstream 

of the mouth of Deep Creek, to its confluence with Kootenay 

Lake (figs. 1 and 2). 

The white sturgeon critical-habitat reach includes the 

lower part of the braided and entire straight reach, but known 

spawning sites are within the straight and meandering reaches. 

During the initial years of monitoring white sturgeon over the 

spawning season (1992-93), mats used by biologist for egg 

collection were placed upstream, within, and downstream of 

the critical-habitat reach, but spawning was seldom detected 

in the upstream and downstream areas. Since 1994, egg mats 

were placed over most of the critical-habitat reach. Since 

1996, egg collection has been limited to the deepest areas of 

the river (V.L. Paragamian, Idaho Department of Fish and 

Game, oral commun., 2005). Paragamian and others (2001, 

2002) identified five primary white sturgeon spawning reaches 

in the Kootenai River in the meandering reach between RKM 

228.0 to 240.0 and concluded that spawning occurs mostly 

in the outsides of meander bends in the thalweg (fig. 3). 

However, during 2001 these same investigators observed 

spawning in the straight reach at RKM 245.1 and 245.7.

 The multidimensional flow model was developed for 

the 17.5-km critical-habitat reach between RKM 228.4 and 

RKM 245.9, and includes all observed spawning sites (fig. 2). 

The model reach was subdivided into two reaches to reflect 

the distinct type of sediment forming the river substrate: (1) 

the straight reach which has a sand, gravel, cobble substrate 

between the upstream model boundary (RKM 245.9) and the 

upstream end of Ambush Rock (RKM 244.6); and (2) the 

meandering reach which primarily consists of a sand substrate 

between upstream end of Ambush Rock and the downstream 

model boundary (RKM 228.4). In addition, the model reach 

was divided into three velocity zones based on the velocity 

structure characteristics within each zone, as discussed in the 

section Streamflow Velocity.

Description of the Study Reach 
near Myrtle Creek displays morphology typical of meander 

bends, with the thalweg along the outside of the bend and 

point bars along the inside of the river bend (Henderson, 1966, 

figs. 10-25). In contrast, near the upstream end of Shorty 

Island between RKM 229.97 and RKM 230.45, the thalweg 

is in the center of the channel and is incised in lacustrine clay 

and silt (Barton, 2004, fig. 23P). The thalweg is on the outside 

of the river bend in the rest of this reach. Variations in channel 

curvature, morphology, and grain size over the model reach 

are important considerations in constructing a flow model 

that can provide spatially distributed information for linkage 

to biological data. The multidimensional model used here is 

sufficiently general to address these variations.

The width of Kootenai River in the model reach ranges 

from about 65 to 255 m when streamflow is below flood stage. 

This reach includes two major tributaries, Deep Creek at RKM 

240.25 and Myrtle Creek at RKM 234.63. Channel geometry 

in the reach varies greatly. The channel is shallow and straight 

between the U.S. Highway 95 Bridge and Ambush Rock and a 

few gravel bars are exposed at low flow; downstream of Deep 

Creek, it meanders and divides around Shorty Island, between 

RKM 229.6 and RKM 231.45. Morphology of the Kootenai 

River near the mouth of Myrtle Creek and at Shorty Island 

is distinct. Near Myrtle Creek, the river forms an S-shaped 

meander and has a maximum width of 200 m. Shorty Island 

is in a gentle meander and divides the flow into a main and 

a secondary channel over its 1,400-m length. Kootenai River 

ID91Z00_fig03

0

5

10

15

20

25

30

35

40

228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246

RIVER KILOMETER NUMBER OF SPA

WNING EVENTS AND SPA

WNING EVENTS PER UNIT OF 

MONITORING EFFORT (X 10,000)

-20,000

-15,000

-10,000

-5,000

0

5,000

10,000

15,000

20,000

CUMULATIVE EFFORT (HOURS)

SPAWNING EVENTS

PER UNIT OF MONITORING 

EFFORT (SEPUE) X 10,000

NUMBER OF

SPAWNING EVENTS

CUMULATIVE EFFORT (HOURS)

DEEP

CREEK

MYRTLE

CREEK SHORTY ISLAND

AMBUSH

ROCK

River Kilometers 229.6 - 231.45 River Kilometer 234.63 River Kilometer 240.25 River Kilometers 244.1 - 244.6

Figure 3. Location and number of white sturgeon spawning events and spawning events per unit effort on the Kootenai 

River near Bonners Ferry, Idaho, 1994 to 2001.

(Paragamian and Wakkinen, Idaho Department of Fish and Game, written commun., 2005.)

 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Physical Characteristics of the White 

Sturgeon Critical-Habitat Reach of the 

Kootenai River 

Application of a 2- or 3-dimensional flow model to 

a river like the Kootenai requires streamflow information, 

topography and bathymetry with sufficient detail to 

characterize the channel, water-surface elevations for boundary 

conditions, substrate grain-size, and bedform information for 

characterization of roughness, and, ideally, measurements of 

water-surface elevation and velocity to calibrate and validate 

the model. Physical characteristics used in this study are based 

on data from previous studies, historical USGS data, and data 

collected by USGS in the critical-habitat reach during 2000-04 

as part of this study. Most of the historical data on streamflow 

and sediment regime are from 1965 through 2004; therefore, 

the construction and calibration of the flow model for the 

critical-habitat reach are based on data from that period. 

Streamflow

One of the most essential model inputs both for 

determining model results and for relating results to biological 

observations is discharge in the river, or streamflow. A 

significant part of streamflow information used for model 

construction is based on records from the Bonners Ferry 

stage-gaging station (12309500) at RKM 245.9, the Tribal 

Hatchery stage, velocity, and streamflow-gaging station 

(12310100) at RKM 241.3, the Klockmann Ranch stagegaging station (12314000) at RKM 224.0, the Copeland stage 

and streamflow-gaging station (12318500) at RKM 198.2, 

the Boundary Creek stage and streamflow-gaging station 

(12321500), which empties into Kootenai River at RKM 

170.6, and the Porthill stage and streamflow-gaging station 

(12322000) at RKM 170.3. Typically, model runs can be 

constructed based on streamflow and water-surface elevation 

from a single measurement site on the mainstream and 

appropriate streamflow information from major tributaries, but 

the influence of backwater effects from Kootenay Lake on the 

study reach makes multiple gaging station locations important 

for this model. 

The operation of Corra Linn Dam and Libby Dam also 

affect backwater conditions. The altitude of the river is about 

532 m at its confluence of Kootenay Lake, located behind 

Corra Linn Dam and about 235 km downstream of Libby 

Dam (fig. 1). Corra Linn Dam was completed in 1931 and is 

operated for hydroelectric power, which affects water levels in 

Kootenay Lake and, consequently, in the backwater-affected 

reach of Kootenai River (Duke and others, 1999). The river 

channel upstream of the dam at Grohman Narrows was 

deepened in 1939 to help maintain a lower lake water-surface 

elevation at Nelson and, thus, a lower river water-surface 

elevation at Bonners Ferry (Pacific Watershed Institute, written 

commun., 1999). Kootenay Lake creates backwater conditions 

in Kootenai River to a variable point upstream of the mouth 

of Deep Creek (RKM 240.25) near Bonners Ferry. During 

May, June, and early July, when lake water-surface elevation 

and river discharge are high, backwater conditions can extend 

several kilometers upstream of the U.S. Highway 95 Bridge 

(RKM 245.9) at Bonners Ferry (fig. 2). During periods of 

low streamflow, backwater conditions diminish and freeflowing water may extend a few kilometers downstream of the 

U.S. Highway 95 Bridge. A detailed analysis of the contact 

location between the free-flowing river and backwater under 

a range of streamflow conditions is presented in Berenbrock 

(2005). Construction of Libby Dam began in 1966, and Lake 

Koocanusa was officially impounded behind the dam on 

March 21, 1972. Libby Dam is operated for flood protection, 

hydroelectric power, and recreation. Streamflow and watersurface elevation boundary conditions used in the model 

depend significantly on the operation of both dams.

The pre-Libby Dam-era flow regime for Kootenai 

River during the period of suspended sediment record at the 

Copeland gaging station (12318500), 1966-71, is characterized 

by peak streamflows resulting from spring snowmelt from late 

April through mid-July (fig. 4). During the pre-Libby Dam 

era, median annual peak streamflow was about 2,237 m3/s. 

A slow recession of streamflow generally started in midJune and stabilized in September. The annual median base 

streamflow during October through February was 88.0 m3/s. 

The average cross-sectional velocity for 62 measurements 

from the cableway at the Copeland gaging station ranged from 

0.06 to 1.21 m/s. 

The Libby Dam-era flow regime for Kootenai River 

during the period of suspended-sediment record at the 

Copeland gaging station, 1973-82 (fig. 4), is characterized 

by median annual peak streamflows of about 600 m3/s, 

less than one-third of the pre-Libby Dam value. Long 

periods of sustained higher flows were during the autumn 

and winter, reflecting the greater demand for hydroelectric 

power generation. Average cross-sectional velocity during 

83 measurements from the cableway at the Copeland gaging 

station ranged from 0.11 to 0.80 m/s. The peak cross-sectional 

velocity during the Libby Dam era was about one-half that of 

the pre-Libby Dam era. 

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 
Figure 4. Annual median daily streamflow and suspended-sediment load for the pre-Libby Dam era (1966–71) 

and Libby Dam era (1973–82) and annual streamflow and suspended-sediment load, 1966–82, Kootenai River at 

Copeland, Idaho.

(Data from U.S. Geological Survey streamflow-gaging station 12318500; from Barton, 2004.) ID91Z00_fig04 MEDIAN DAILY STREAMFLOW, IN CUBIC METERS PER SECOND STREAMFLOW, IN BILLIONS OF CUBIC METERS PER YEAR

MEDIAN DAILY SUSPENDED-SEDIMENT LOAD, IN METRIC TONS PER DAY SUSPENDED-SEDIMENT LOAD, IN THOUSANDS OF METRIC TONS PER YEAR

YEAR

MONTH

PRE-LIBBY DAM ERA, 1966–71

LIBBY DAM ERA, 1973–82

A.

C. 1966–82 

B.

3,000

2,400

1,800

1,200

600

0

1,000

800

600

400

200

0

30

25

20

15

10

5

0

3,000

2,500

2,000

1,500

1,000

500

0

55,000

44,000

33,000

22,000

11,000

0

13,750

11,000

8,250

5,500

2,750

0

1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982

 Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

Streamflow

Suspended-sediment load

 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 5. Streamflow, water-surface elevation, and water-surface slope of the white sturgeon critical-habitat reach of the 

Kootenai River, Bonners Ferry, Idaho, and water-surface elevation of Kootenay Lake, 1965–2003.

The difference in water-surface elevation between 

the gaging station at Klockmann Ranch (12314000), at the 

downstream model boundary of the critical-habitat reach of 

the Kootenai River, and Kootenay Lake (08NH064) remained 

small over the period of streamflow record, 1965-2003, at 

the Porthill gaging station (fig. 5). The slope of the reach was 

computed as the water-surface elevation at Bonners Ferry 

(12309500) minus water-surface elevation at Klockmann 

Ranch divided by the distance between the two gaging 

stations. Backwater conditions in the critical-habitat reach 

result in gentle water-surface slopes (fig. 5). Slope is reported 

as a reach average that approximates conditions in the criticalhabitat reach. Median daily slope in the reach during the 

pre-Libby Dam era (1965-71) was 0.000018 and during the 

Libby-Dam era (1973-2003) was 0.000027. The difference in 

daily water-surface elevation between Klockmann Ranch and 

Queens Bay on Kootenay Lake during the pre-Libby Dam era 

was 0.59 m and during the Libby-Dam era was 1.13 m.

To augment existing water-surface elevation and 

streamflow data, the USGS began operating gaging station 

12310100 at the KTOI Tribal Hatchery near Bonners Ferry 

at RKM 241.5, in October 2002. The gaging station was 

equipped with an acoustic Doppler velocity meter. Streamflow 

at the gaging station during the period of record through April 

12, 2004, ranged from 120 to 892 m3/s and average crosssectional velocity ranged from 0.17 to 0.75 m/s.

Since the mid-1990s, the U.S. Fish and Wildlife Service 

has requested that Kootenai River flows be increased during 

white sturgeon spawning in May and June in an attempt 

to help re-establish recruitment. Kootenai River flows are 

augmented with additional release of water from Libby Dam; 

however, flow during spawning season is less than one-half 

that of the pre-Libby Dam era. 

Additional information about streamflow, as well as 

sediment-transport regime, in Kootenai River can be obtained 

in reports by Berenbrock and Bennett (2005) who developed 

the 1-dimensional sediment-transport model of the white 

sturgeon critical-habitat reach, Berenbrock (2005), who 

developed a 1-dimensional hydraulic model of Kootenai 

River throughout Idaho, and Barton (2004), who analyzed 

streamflow and suspended-sediment load measured at the 

Copeland gaging station (12318500) during 1966-82.

500

1,000

1,500

2,000

2,500

3,000

1/1/651/1/661/1/671/1/68

12/31/6812/31/6912/31/7012/31/7112/30/7212/30/7312/30/7412/30/7512/29/7612/29/7712/29/7812/29/7912/28/8012/28/8112/28/8212/28/8312/27/8412/27/8512/27/8612/27/8712/26/8812/26/8912/26/9012/26/9112/25/9212/25/9312/25/9412/25/9512/24/9612/24/9712/24/9812/24/9912/23/0012/23/0112/23/0212/23/03

Porthill gaging station (12322000) minus Boundary Creek gaging station (12321500)

530

532

534

536

538

540

542

544

Klockmann gaging station (12314000), river stage

Queens Bay gaging station (08NH064), lake stage

0.000000

0.000025

0.000050

0.000075

0.000100

Average slope between Bonners Ferry gaging station (12309500)

and Klockmann Ranch gaging station (12314000)

STREAMFLOW, IN CUBIC

METERS PER SECOND

WATER-SURFACE

ELEVATION, IN METERS

(NAVD 88)

WATER-SURFACE SLOPE

NEAR BONNERS FERRY

0

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 
Composition of Channel Substrate 

One goal of the modeling program was to demonstrate 

how the model can be used to link physical characteristics 

of streamflow to biological or other habitat data, such as 

predicting sediment movement for various streamflows. To 

obtain the required information, sediment cores and surface 

sediment samples were collected during this study to refine the 

characterization of the composition of the channel substrate. 

Fifty-one cores of riverbed sediment were collected from 

RKM 245.4 to RKM 228.0 during September 2004. (fig. 6). 

A 7.3-m pontoon coring boat was used for taking vibracores 

and piston cores of sediment beneath the riverbed. Core sites 

were referenced spatially using a global positioning system 

(GPS). Two to four sediment cores were usually taken at a 

cross section of the river. Generally, one core was taken from 

the thalweg and another in shallower water. The vibracoring 

system is equipped with a 0.08-m diameter core barrel that is 

3.66 m long and can recover clay, silt, sand, gravel, and some 

cobble. The maximum substrate penetration by the core during 

data collection was 3.3 m. 

Several gravel bars are in the upper half of the straight 

reach. The substrate is composed of gravel and some cobble, 

some alluvial sand, and a few bedrock outcrops. The river bed 

in the meandering reach is dominated by sand dunes, and the 

substrate consist mainly of fine to medium sand, with minor 

amounts of lacustrine clay and silt that typically are detected 

in the thalweg and along the outside bank of meanders. In 

a few cases, gravel, cobble, and riprap are on the riverbed 

in the meandering reach. Riprap is erosion resistant ground 

cover consisting of large, loose, angular stone. Sediments 

generally are in limited areas along the outside of meander 

bends, where velocities are highest in the bend. At least some 

of these sediments are not naturally occurring and were placed 

to protect the dikes that line the river. Some riprap has rolled 

down the toe of the dike into the channel. In addition, below 

the mouth of Myrtle Creek between RKM 234.20 and 234.60, 

Barton (2004) identified gravel, cobble, and riprap on the 

riverbed that is exposed or buried by a thin layer of sand. The 

source of these gravels and cobbles may be an alluvial fan at 

the base of Cascade Ridge or the sediment that forms the dike. 

Small, isolated gravel lenses buried by a thin layer of sand also 

were identified at RKM 241.6 and 243.8, between Ambush 

Rock and Mission Hill.

Particle-size distribution of the sediment that forms the 

substrate in the critical-habitat reach was measured during 

this study. The Kootenai Tribe of Idaho collected bed-material 

samples between RKM 226 and 244.3 on June 20, 2000. 

These samples were taken with a ponar dredge sampler at 22 

sites located near mid-channel and near the riverbanks (fig. 7). 

In addition, six grab samples were collected from exposed 

gravel bars in the straight reach during March 2002 (fig. 7). A 

subset of 12 samples from the 2000 sampling and 3 samples 

from the 2002 sampling were sent to the USGS Cascades 

Volcanic Observatory Sediment Laboratory for 1⁄2 phi particle 

size analysis. Average particle sizes for the set of samples 

from the meandering reach are D16, 0.15 millimeters (mm), 

D50, 0.23 mm, and D84, 0.33 mm, classified as fine to medium 

sand (0.063 to 0.25 mm, very fine to fine sand; 0.25 to 

0.50 mm, medium sand). Particle-size distribution data (fig. 8), 

along with geologist logs from vibracores and piston cores, 

show that the riverbed in the meandering reach is covered with 

sediment of nearly consistent size. Particle-size distribution 

of these bed-sediment samples is much smaller than in the set 

of samples collected further upstream between U.S. Highway 

95 Bridge and Ambush Rock, where D50 was 15.5 mm, which 

represents gravel- and cobble-size sediment. Studies on the 

white sturgeon in the Lower Columbia River (Parsley and 

Beckman, 1994), suggest that the particle size of substrate 

in the straight reach has poor to moderate suitability for egg 

incubation and in the meander reach has poor suitability. 

Isolated areas in the meander reach may be better suited for 

egg incubation where gravel is present and not buried by sand, 

such as below the mouth of Myrtle Creek between RKM 

234.20 and 234.60 (Barton, 2004). 

10 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID91Z00_fig06

2

95

2

95

Kootenai 

River 

IDAHO

Bonners

Ferry

Myrtle

Creek 

Shorty 

Island 

Lost Creek 

Ambush 

Rock

Ball

Creek 

K O O T E N A I F L A T S 

K O O T

E N A I F L A T S 

Deep

Creek 

Kilometer 230 

Kilometer 235

Kilometer 240 

Kilometer 245 

11-TH 

K3-TH

K5-C

K5-TB

K3-C

11-RB 

SI-1

SI-2 

12-RB

12-TH 

12-LB 

13-TH+C

13-LB

K6-RB

K6-TH

K6-LB

K6.5

K9-LB

K9-C

K9-RB

K13-LB2

K13-LB1

K13-TH

K14-TH

K15.5-TH

K16-C1 K16-C2

K16-LB

K13-RB K11-LB

K11-C

K12-TH1

K12-TH2

K12-LB

K9.5-TH

K9.5-C

K9.5-RB

K10-TH1

K10-TH2

K10-RTH

K10-RC

13-RB

20-RB 

19-RB

19-LofC 19-LB 

SI-6 

19-RofC

SI-4 

SI-5 

SI-3 

21-TH

14-RB

14-TH

23-TH 

22-TH

1-TH 

16-TH 

17-TH 

2-LB 

2-C 2-RB 

4-LofC 

10-RB 

6-C 

5-RB 

4-RB 

4-RofC 

4-LB 

5-C

K20-TH

K18-LB

K18-TH

6-RB 

9-LB 

7-C 8-LB 

5-LB

10-LB2 

10-C 

9-C 8-TH 6-TH

8-RB 

8-RB2 

7-RB 9-RB 

9-RB2 

116° 25' 116° 20'

48°

45'

48°

45' 30”

EXPLANATION

13-LB

K6-RB

TH

RB

LB

C

LofC

RofC

RIVER KILOMETER

SEDIMENT CORE SITE AND NO. —

 Samples taken in 2004

 Samples taken in 2000

 Thalweg

 Right Bank

 Left Bank

 Center

 Left of Center

 Right of Center

Kilometer 235

+

0

0 1 MILE

1 2 3 KILOMETERS

Base from U.S. Geological Survey digital data, 1:100,000, 1983

Universal Transverse Mercator projection, Zone 13

Figure 6. Location of sediment core sites sampled in 2000 and 2004 on the white sturgeon critical-habitat reach of the 

Kootenai River near Bonners Ferry, Idaho.

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 11
ID stress-model_fig07

2

95

95

2

Kilometer 225 

Kilometer 230 

Kilometer 235 

Kilometer 240

Kilometer 245 Kilometer 250 

Myrtle

Creek

Shorty

Island

Lost Creek

Ball

Creek

Ambush

Rock

IDAHO

Bonners

Ferry

S E L K I R K R A N G E 

River 

Kootenai

Deep

Creek 

S9 

S8 

S7 

A-LB

A-MID

B-LB

C-MID

E-RB

E-MID

F-LB F-MID

D-LB D-MID

G-RB

G-MID H-RB

H-MID

I-MID I-RB

J-RB J-MID

K-RB

K-MID

116° 25' 116° 20'

48°

45'

48°

40'

E-MID

E-RB

E-LB

S8

Kilometer 235 +

EXPLANATION

RIVER KILOMETER

DREDGE SAMPLE SITE —

 Middle of Channel

 Right Bank

 Left Bank

SEDIMENT GRAB-SAMPLING

 SITE AND NO.

0

0 1 2 MILES

1 2 3 4 KILOMETERS 

Figure 7. Location of streambed-sediment sampling sites on the white sturgeon critical-habitat reach of the Kootenai River 

near Bonners Ferry, Idaho.

12  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 8. Particle-size distribution for streambed sediment samples taken between river kilometers 228.4 and 245.8 on the white sturgeon 

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho. 

(Kootenai Tribe of Idaho collected samples A through J with ponar dredge. Sample sites shown in figure 7.)

ID91Z00_fig08

SILT SAND GRAVEL COBBLE

0

10

20

30

40

50

60

70

80

90

100

0.01 0.1 1 10 100

SIEVE SIZE, IN MILLIMETERS

PERCENT FINER

J-MID

J-RB

I-MID

I-RB

H-MID

H-RB

G-MID

G-RB

F-LB

F-MID

E-MID

E-RB

D-MID

D-LB

C-MID

B-LB

A-MID

A-LB

S-7

S-8

S-9

Dredge-sample sites: sample from

MID,middle of channel;

RB, near right bank; and, 

LB, near left bank

Sediment-Transport Regime

Although information regarding the sediment-transport 

regime is not required for application of a multidimensional 

flow model, this information can be useful for understanding 

how changes in sediment supply during various streamflows 

might affect channel morphology or other physical 

characteristics of the system. During snowmelt runoff in the 

pre-Libby Dam era, sediment data collected at the USGS 

gaging station at Copeland (12318500) indicate that large 

amounts of suspended sediment were transported through the 

white sturgeon critical-habitat reach. The annual suspendedsediment load leaving the Kootenai River critical-habitat reach 

decreased dramatically after the closure of Libby Dam in 

1972. During the pre-Libby Dam era, annual average load at 

the Copeland gaging station from 1966 to 1971 was 1,740,000 

metric tons per day (mt/d) and annual median daily load 

ranged from 14 to 48,700 mt/d, but after dam closure, annual 

average load from 1973 to 1982 was 190,000 mt/d and annual 

median daily load ranged from 53 to 1,560 mt/d (fig. 4). 

Suspended-sediment transport during the Libby Dam era was 

minimal, about 11 percent of the average annual pre-Libby 

Dam era amount. This reduction was caused by the influence 

on the flow regime of dam regulation for flood control and 

power demand, as discussed above. In addition to the effects 

of changes in streamflow, less sediment was available for 

transport because 70 percent of the basin is upstream of Libby 

Dam (Barton, 2004).

During 2002 and 2003, depth-integrated cross-sectional 

suspended-sediment samples were collected at the upstream 

end of the critical-habitat reach near Fry Creek and at the 

downstream end of the reach near Ball Creek, and are described 

in detail in Berenbrock and Bennett (2005). In addition, during 

2002 and 2003 a series of single depth-integrated suspendedsediment samples was collected from the U.S. Highway 95 

Bridge. Berenbrock and Bennett computed a suspendedsediment transport curve and a total-sediment transport curve 

for the upstream end of the modeling reach at the U.S. Highway 

95 Bridge using these data. For streamflow simulations of 170, 

547, 1,132, and 1,708 m3/s, the suspended-sediment transport 

curve indicated estimated sediment loads of 132, 1,590, 6,670, 

and 15,400 mt/d, respectively; the total-sediment transport 

curve indicated estimated sediment loads of 148, 2,050, 9,260, 

and 22,400 mt/d, respectively. Berenbrock and Bennett (2005) 

also computed a sediment-transport curve for total suspended 

sediment for the downstream end of the white sturgeon 

critical-habitat reach near Ball Creek.

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 13
River Channel Geometry

Channel geometry data were collected for the criticalhabitat reach of Kootenai River and then used to (1) map 

bathymetry for use in the flow modeling, (2) characterize 

bedform geometry, and (3) determine degradation and 

aggradation of the riverbed. River bathymetry was mapped 

during 2002, 2003, and 2004, and the data were used as input 

to the multidimensional flow model. Geometry, amplitude, 

and wavelength of dunes and other bedforms were monitored 

at five longitudinal-profile sites and channel degradation and 

aggradation were monitored at five cross-section sites on the 

reach. During collection of channel-geometry data, streamflow 

and river water-surface elevation fluctuated and generally 

represented unsteady flow conditions (fig. 9). 

Bathymetry and Streambank Topography

Bathymetry for the modeling reach was based on mapping 

conducted during June 2002, April 2003, and August 2004. 

Bathymetric data collection details are provided in Barton 

and others (2004) and briefly summarized here. Prior to data 

collection, survey-control stations with a horizontal and vertical 

accuracy of less than 0.03 m were established along Kootenai 

River using survey-grade GPS equipment. Bathymetric data 

were obtained by interfacing real-time GPS equipment with a 

survey-grade echo sounder (Barton and others, 2004, fig. 4). 

Manufacturer-reported accuracy of real-time GPS surveying 

equipment is ±0.020 m plus 1 part per million (ppm) in the 

vertical and ±0.010 m plus 1 ppm in the horizontal, (http://

trl.trimble.com/docushare/dsweb/Get/Document-163620/; 

accessed July 25, 2005), and the accuracy of the echo sounder 

was consistently less than ±0.031 m. Taking into account all 

sources of mapping error, the bathymetry and streambank 

topography was mapped with a horizontal accuracy of ±0.050 

m and ±0.601 m and a vertical accuracy of ±0.030 m and 

±0.091 m, respectively (Barton and others, 2004). Vertical 

coordinate information was referenced to the North American 

Vertical Datum of 1988 (NAVD 88). Horizontal coordinate 

information was referenced to the North American Datum of 

1983 (NAD 83), Idaho Transverse Mercator—North American 

Datum 1983/1998 Idaho West, in meters.

During 2002 and 2003, water depth was measured with 

a single-beam echo sounder (Innerspace Technology, Inc., 

Model 448). About 260 cross sections and two to seven 

longitudinal lines were surveyed in the modeling reach. 

Spacing between cross sections ranged from less than 10 

to about 50 m. During 2004, water depth was measured 

with a multi-beam echo sounder (Ross Model 875-4 with 

four channels). Spacing between each of the four sounding 

transducers was 2.8 m. A series of longitudinal lines was 

surveyed in the modeling reach between RKM 245.9 and 

RKM 236.8 and between RKM 232.5 and RKM 228.4. 

Longitudinal lines generally were parallel and spaced 

relatively close together. About 80 percent of the river 

bottom in these two reaches was surveyed. The multi-beam 

echo sounder provided a much more closely spaced set of 

bathymetric data than the single-beam system, allowing 

development of a model with smaller computational cells and 

greater detail.

Streambank shots were taken at breaks in topographic 

slope using a laser range-finder (Laser Technology Impulse 

200LR) and angle encoder (Laser Technology Mapstar Angle 

Encoder System) interfaced with the Trimble 5700 GPS. 

14  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 9. Daily mean flow and water-surface elevation for the white sturgeon critical-habitat reach of Kootenai River near Bonners Ferry, Idaho, 

2002 and 2003. 

_fig09

0

500

1,0001,5002,000

2002/ 1/ 3

2002/ 13/ 3

2002/ 03/ 4

2002/ 03/ 5

2002/ 92/ 6

2002/ 92/ 7

2002/ 82/ 8

2002/ 72/ 9

2002/ 72/ 01

2002/ 62/ 11

2002/ 62/ 21

3002/ 52/ 1

3002/ 42/ 2

3002/ 62/ 3

3002/ 52/ 4

3002/ 52/ 5

3002/ 42/ 6

3002/ 42/ 7

3002/ 32/ 8

3002/ 22/ 9

DNOCES REP SRETE MCI BUC NI , WOLF MAERTS

530532534536538

) 88 DVAN( SRETE MNI , EGATS

Streamflow: Porthill gage12322000 minus Boundary Creek gage (12321500),

3/01-10/09/2002, and Tribal Hatchery gage (12310100), 10/10/2002-9/30/2003

Stage at Bonners Ferry gage (12309500)Stage at Klockmann Ranch gage near Bonners Ferry (12314000)Stage at Tribal Hatchery gage near Bonners Ferry (12310100)

DATE

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 15
Dunes and Other Bedforms

Geometry, amplitude, and wavelength of dunes and other 

bedforms were monitored at five sites in the modeled reach 

(fig. 10). The sites were monitored on May 24, June 6, July 

23, and September 4, 2002, when streamflows were 1,150, 

1,110, 663, and 229 m3/s. Each site consisted of a longitudinal 

profile in the center of the channel with lengths ranging from 

216 to 329 m. An acoustic Doppler current profiler (ADCP, 

RD Instruments Rio Grande model) was mounted to a survey 

vessel and used to measure velocity, river depth, and distance 

traveled. The upstream end of each longitudinal profile was 

located with a general purpose GPS. Sites F-F ́, I-I ́, and J-J ́ 

are where the river forms a relatively straight channel and sites 

G-G ́ and H-H ́ are in the thalweg of meander bends (fig. 10). 

Sites G-G ́ and H-H ́ were not analyzed or included in the 

model because maintaining position on a profile was more 

difficult at sites in a meander bend as compared to sites in a 

straight channel.

Longitudinal-profile data indicate that Kootenai River 

bedform geometry is linked to streamflow. In general, dune 

bedforms have the greatest amplitude (vertical relief) at the 

low streamflow regime when flow is steady, and amplitude 

generally decreases with increasing streamflow until the dunes 

washout at the high streamflow regime and form a plane 

bed (fig. 11 and table 1). This observation is consistent with 

research on the evolution of sand bedforms and streamflow 

regime (Henderson, 1966, chap. 10.2; Simons and Richardson, 

1961). Dunes exhibited the greatest amplitude during the 

229 m3/s streamflow of September 4, 2002: the average 

amplitude for longitudinal profiles F-F ́, I-I ́, and J-J ́ was 

0.7 m and the largest amplitude, 1.4 m, was observed at site 

I-I ́. During high streamflow, dunes were washed out and 

a flat plane bed was formed along most of the longitudinal 

profile at sites F-F ́ and I-I ́ on May 24, 2002, and at site 

J-J ́ on June 6, 2002. Average dune wavelength at profile 

F-F ́ was 12.2 m on May 24, 2002, and 14.2 m on July 23, 

2002. In contrast, average dune wavelength at profile F-F ́, 

I-I ́, and J-J ́ was 20.42 m on September 4, 2002,. These data 

provide a generalized characterization of the relation between 

streamflow and bedform geometry; additional data would be 

needed to provide a more thorough understanding.

River Channel Degradation and Aggradation

Degradation and aggradation of the Kootenai River 

channel in the critical-habitat reach were monitored at five 

channel cross sections: A-A ́, B-B ́, C-C ́, D-D ́, and E-E ́ 

(figs. 10 and 12). The sites also were monitored on May 24, 

June 6, July 23, and September 4, 2002, when streamflows 

were 1,150, 1,110, 663, and 229 m3/s, respectively. Channel 

cross section were measured with an ADCP using datacollection methods discussed in the section Dunes and Other 

Bedforms. Channel cross section surveys show that the 

thalweg appears stable during low flows and high flows with 

little channel aggradation and degradation. In the thalweg of 

sections C-C ́, D-D ́, and E-E ́, less than 1 , 1.2 , and 0.6 m 

of change was measured in riverbed elevation, respectively 

(fig. 12). Changes in elevation at each cross section are on 

the order of measured bedform amplitudes, and because there 

is no systematic change in elevation along either the thalweg 

or the channel margins from low to high flow, changes likely 

represent migration of bedforms on the channel bottom. It 

appears that the river channel is fairly stable, at least for 

the range of observed streamflows. This observation can 

be used to justify merging topographic data sets that were 

measured over various streamflows. Furthermore, channel 

stability indicates that some justification exists for modeling 

flow patterns for streamflows other than when collecting 

bathymetric data. 

Table 1. Amplitude and wavelength of dune bedforms in the white sturgeon critical-habitat reach of the Kootenai River, near Bonners Ferry, Idaho.

[Location of longitudinal profiles shown in figure 8. Longitudinal profiles: amplitude, dune vertical relief; wavelength, dune length; FI, flat to irregular 

bedforms; F, flat bedforms. Abbreviations: m3/s, cubic meter per second; ft3/s, cubic foot per second; m, meter; ft, foot; ND, no data]

Date

Longitudinal profile F-F’ Longitudinal profile I-I’ Longitudinal profile J -J’

Streamflow Average 

amplitude

Average 

wavelength

Average 

amplitude

Average 

wavelength

Average 

amplitude

Average 

wavelength

(m3/s) (ft3/s) (m) (ft) (m) (ft) (m) (ft) (m) (ft) (m) (ft) (m) (ft)

05-24-2002 1,150 40,700 0.20 0.64 12.2 40.0 FI FI F F 0.21F 0.7F F F

06-06-2002 1,110 39,100 .30 .99 14.0 46.1 ND ND ND ND .12F .4F F F

07-23-2002 663 23,400 .51 1.68 18.9 62.0 0.61 2.00 19.4 63.6 .23 .76 17.9 58.7

09-04-2002 229 8,070 .69 2.27 20.4 67.0 .84 2.75 22.4 73.4 .46 1.50 18.4 60.4

16  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 10. Location of acoustic Doppler current profiler cross sections and longitudinal profiles for monitoring riverbed 

stability and bedforms on the white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho.

ID91Z00_fig10

2

95

95

2

Burlington

Northern

Santa Fe

Railroad

Union

Pacific

Railroad

Pacific

Union

Railroad

BNSF Railroad

River

IDAHO

Bonners

Ferry

Deep

Creek

Myrtle Creek

Shorty

Island

Lost Creek

Ball

Creek

Ambush

Rock

Mission

Hill

S E L K I R K R A N G E

Kootenai

K O O T E N A I F L A T S

K O O T

E N A I F L A T S

Downstream

boundary for

multidimensional

model

Upstream

boundary for

multidimensional

model

Base from U.S. Geological Survey digital data, 1:100,000, 1983

Universal Transverse Mercator projection, Zone 13

F–F’

I–I’

H–H’

J–J’

G–G’

E’

E

D’

D

C’ C

B’

B A’ A

Kilometer 225

Kilometer 230

Kilometer 235

Kilometer 240

Kilometer 245

Kilometer 250

116° 25' 116° 20'

48°

45'

48°

40'

EXPLANATION

AREA ABOVE FLOOD PLAIN

RIVER KILOMETER

ACOUSTIC DOPPLER CURRENT PROFILER

 CROSS SECTION AND NO. —

 May through September 2002

ACOUSTIC DOPPLER CURRENT PROFILER

 LONGITUDINAL PROFILE 

 AND NO. — May through September 2002

Kilometer 235 +

A-A’

G-G’

0

0 1 2 MILES

1 2 3 4 KILOMETERS

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 17
g11

523524525526527528529

523524525526527528529

SRETE MNI , DEB REVI RF O NOI TAVELE

523524525526527528529

0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320

DISTANCE FROM UPSTREA

M END OF LONGITUDINAL SECTION, IN METERS

May 24, 2002, streamflow 1,150 cubic meters per second (40,700 cubic feet per second)June 26, 2002, streamflow 1,110 cubic meters per second (39,100 cubic feet per second)July 23, 2002, streamflow 663 cubic meters per second (23,400 cubic feet per second)September 4, 2002, streamflow 229 cubic meters per second (8,070 cubic feet per second) F F'

J' J

I' I

Figure 11. Changes in bedforms along longitudinal profiles measured with an acoustic Doppler current profiler in the white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, 2002. (Location of sections shown in figure 8.)

18  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID 91Z00_fig12

520

522

524

526

528

530

532

534

536

DISTANCE FROM LEFT BANK TO RIGHT BANK, IN METERS

D D'

520

522

524

526

528

530

532

534

536

B B'

520

522

524

526

528

530

532

534

536

0 20 40 60 80 100 120 140 160 180 200

520

522

524

526

528

530

532

534

C C'

Debris

520

522

524

526

528

530

532

534

536

May 24, 2002, streamflow 1,150 cubic meters per second (40,700 cubic feet per second)

July 23, 2002, streamflow 663 cubic meters per second (23,400 cubic feet per second)

June 26, 2002, streamflow 1,110 cubic meters per second (39,100 cubic feet per second)

September 4, 2002, streamflow 229 cubic meters per second (8,070 cubic feet per second)

A A'

E E'

Left bank of river is located about 200 meters below mouth of Mrytle Creek

ELEV

ATION OF RIVER BED, IN METERS

EXPLANATION

Figure 12. Aggradation and degradation of streambed at five cross sections of the white sturgeon critical-habitat reach of the 

Kootenai River near Bonners Ferry, Idaho, 2002. 

(Location of sections shown in figure 8.)

Physical Characteristics of the White Sturgeon Critical-Habitat Reach of the Kootenai River 19
Construction of the Multidimensional 

Flow Model

The USGS multidimensional surface-water modeling 

system (MD_SWMS) was used in this study to simulate 

water-surface elevation, velocity, and boundary (bed) shear 

stress. When used with subsidiary methods, the flow model 

also can simulate the motion of sediment on the riverbed 

and morphologic evolution of the bed. Potential uses for 

the model include simulations of (1) flow and sedimenttransport conditions at known or inferred spawning locations, 

and (2) sediment mobility and the potential for erosion or 

deposition in the channel near proposed stable substrate 

enhancements (Barton and Ireland, 2000). 

MD_SWMS is a Graphical User Interface (GUI) 

developed by the USGS (McDonald and others, 2001; 

McDonald, Nelson, and Bennett, in press; McDonald, Nelson, 

Kinzel, and Conaway, in press) for hydrodynamic models. 

FaSTMECH is one computational model within MD_SWMS 

and was developed at the USGS (Nelson and McDonald, 

1997; Thompson and others, 1998; Lisle and others, 2000, 

Nelson and others, 2003; McDonald, Nelson, and Bennett, 

in press; McDonald, Nelson, Kinzel, and Conaway, in press). 

FaSTMECH includes a 2-dimensional, vertically averaged 

model and a sub-model that calculates vertical distribution 

of the primary velocity and the secondary flow about the 

vertically averaged flow. This so-called 2.5-dimensional 

approach has been shown to adequately simulate the velocity 

field, bed shear stress, and resulting patterns of erosion and 

deposition where secondary flows are significant without the 

complexity of a fully 3-dimensional model.

Minimum data requirements for the model include 

channel geometry, streamflow at the upstream boundary, and 

water-surface elevation at the downstream boundary. Physical 

assumptions of the model are that (1) flow is steady, (2) flow is 

incompressible, (3) flow is hydrostatic (vertical accelerations 

are neglected), and (4) turbulence is adequately treated by 

relating Reynolds stresses to shear using an isotropic eddy 

viscosity (Nelson and others, 2003). Additional information on 

the interface and the model used for this study can be found in 

McDonald and others (2001), McDonald, Nelson, and Bennett 

(in press), McDonald, Nelson, Kinzel, and Conaway (in press), 

Nelson and others (2003), and Nelson and Smith (1989a). 

Computational Grid and Bathymetric 

Interpolation

The computational grid used in FaSTMECH is a 

curvilinear orthogonal coordinate system with a user-defined 

centerline. The grid centerline is defined interactively to 

approximate mean flow streamline of the modeling reach 

(Nelson and others, 2003). The computational grid used 

to model the Kootenai River was 17,525 m in length with 

3,505 nodes in the downstream direction and 800 m in width 

with 161 nodes in the cross-stream direction, forming an 

approximately 5.0- by 5.0-m grid (fig. 13). 

Measured topography is mapped to the coordinates of 

the computation grid through a “nearest-neighbor” method. 

A search bin is defined with a downstream length and crossstream width that forms a curved rectangle whose geometry 

follows the local grid curvature and is centered on the node 

coordinate being mapped. By choosing the cross-stream 

and streamwise extent of the search bin judiciously, the user 

can tune the interpolation to treat situations where slopes 

in the cross-stream direction are steeper than those in the 

streamwise direction, which is frequently true in alluvial 

rivers. Surveyed points within the bin are used to interpolate 

survey data to the node. If the search bin does not contain 

any surveyed points, the search bin is doubled in dimension 

until one or more surveyed points are found. Elevation of the 

points within the bin are weighted by distance from the survey 

point to the computational node and averaged to obtain a 

value for each node of the computational grid. This approach 

works well where the channel banks are nearly parallel to the 

computational grid centerline. This is effectively true for most 

of the modeling reach except around Shorty Island, where the 

Kootenai River diverges into two channels and their banks 

trend at angles across the centerline of the model grid. This 

was overcome by first separating the channel for the purposes 

of topographic interpolation into two separate reaches: the 

main channel and a secondary channel around Shorty Island. 

A curvilinear grid following the secondary channel around 

Shorty Island, with a 5.0-m spacing in the downstream and 

cross-stream dimensions near the grid centerline, was created 

to map the topography in this region (fig. 13). Surveyed 

topography was mapped to this grid based on a search bin with 

a length of 45.0 m in the downstream direction and a width 

of 3.0 m in the cross-stream direction. For the main channel, 

20 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 13. Nodes forming an approximately 5.0-by-5.0-meter grid in the multidimensional flow model at the upstream end of Shorty Island in the white sturgeon critical-habitat reach of 

the Kootenai River near Bonners Ferry, Idaho.

ig13

Major Channel Shorty Island Minor Channel

Streamflow

116

Model boundary

°22’30”

48°

45'

Construction of the Multidimensional Flow Model  21
the surveyed data was separated into three separate reaches 

for the purposes of topographic interpolation: (1) between 

RKM 245.9 and RKM 237.5 in the upper part of the modeling 

reach, where multi-beam bathymetric data were collected 

during 2004 and single-beam bathymetric data collected 

during 2002 and 2003; (2) between RKM 231.9 and RKM 

237.5 in the center of the modeling reach, where only singlebeam bathymetric data were collected during 2002-03; and 

(3) between RKM 231.9 and RKM 228.4 near Shorty Island, 

where multi-beam bathymetric data were collected during 

August 2004 in addition to the single-beam bathymetric data 

collected during 2002 and 2003. Surveyed topography was 

mapped to 5.0-m grids created for each of these three regions 

using a search bin with lengths of 25.0, 45.0, and 20.0 m 

for reaches (1), (2), and (3), respectively, in the downstream 

direction, all with a width of 3.0 m and a weighting exponent 

of 1.5. The resulting topography mapped to all four grids 

(one for the Shorty Island secondary channel and three from 

the main channel) were combined with the original measured 

topography to form a densely spaced set of topographic data, 

thereby filling in some sparse areas in the surveyed data. The 

dense topographic data then were used to map the topography 

to the actual computational grid (a 5.0-m by 5.0-m grid at 

the centerline of the coordinate system) using a search bin 

of 5.0 m in length and width and a weighting exponent of 

1.5. Although this overall process seems complicated, it 

was the simplest way to deal with interpolation to the model 

coordinate system, taking into account variations in the 

channel planform and density of the surveyed topographic 

data. Model coordinates and elevations are in the NAD 83 

datum, Idaho Transverse Mercator projection, and NAVD 88, 

respectively.

Streamflow Velocity at the Upstream Model 

Boundary 

Streamflow velocity at the upstream boundary of the 

model grid have a significant effect on the simulation of 

flow for roughly the upper kilometer of the modeling reach. 

Specified velocity boundary conditions at the upstream model 

boundary were based on available streamflow measurements 

made at a cross section at the U.S. Highway 95 Bridge using a 

Price AA current meter (fig. 14). A streamflow of 1,260 m3/s 

was measured on June 7, 1996, by making 35 current meter 

measurements in the cross section. A streamflow of 776 m3/s 

was measured on April 16, 2002, by making 33 current meter 

measurements in the cross section. The cross-section medians 

of the vertically averaged velocities for measurements 

made on April 16, 2002, and June 7, 1996, were 0.71 and 

0.78 m/s, respectively. Field measurements show that the 

highest velocities and largest streamflows are focused between 

the mid channel and left bank (facing downstream). Vertically 

averaged velocities at each measurement point across the 

channel for the 1996 and 2002 streamflow measurements 

were combined to produce an average upstream-velocity 

boundary condition and then normalized so that the distance 

and velocity magnitude ranged from 0.0 to 1.0. For all flow 

scenarios the model takes the normalized velocity distribution, 

stretches it to fit the wetted length of the specified boundary in 

the model and then amplifies the normalized velocity to satisfy 

the prescribed streamflow for the model run. The cross-stream 

velocity at the upstream model boundary was assumed to be 

zero, in good agreement with observations. 

Water-Surface Elevation at the Downstream 

Model Boundary

In addition to the streamflow-velocity condition at 

the upstream boundary, the model requires a water-surface 

elevation (stage) at the downstream end of the modeled 

reach. Boundary conditions for water-surface elevation at the 

downstream model boundary typically were computed by 

interpolation of the water-surface elevation at the Bonners 

Ferry gaging station (12309500) and Klockmann Ranch 

gaging station (12314000). In some cases, the lower boundary 

conditions were set using the 1-dimensional model described 

by Berenbrock (2005). 

During model runs, including calibration, channel 

curvature at the downstream model boundary caused 

recirculation currents at the model boundary, which is 

problematic, given that the momentum flux and water-surface 

elevation downstream of the model reach were unknown. To 

address this common problem, the MD_SWMS grid extension 

module was used to extend and gradually straighten the grid in 

the downstream direction by 60 nodes over a distance of 300 

m to eliminate recirculation regions at the downstream end of 

the model reach. The grid extension does not alter the flow 

solution in the region of interest. The alternative would have 

been to survey additional topography to allow the downstream 

end of the model reach to be located in a region without 

recirculation, but this would have been costly and would not 

have had any effect on the model solutions.

Model Calibration

Calibration is the process of adjusting model parameters 

within reasonable limits to obtain the best fit of the model 

results to measured data. This process involves repeatedly 

adjusting a parameter, running the model, and inspecting 

differences between model results and measured data with 

the objective of minimizing the difference. In this study, 

calibration consisted of comparing the differences between 

simulated and observed water-surface elevations at selected 

sites, and adjusting the drag coefficient to match observed 

slopes. 

22  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
The model was calibrated to 14 historical streamflow 

conditions (table 2) that ranged from 157 to 2,540 m3/s. 

Selection of historical streamflow conditions used for 

model calibration was based on two criteria: (1) historical 

streamflows should be evenly distributed between 141.6 m3/

s and 2,548.9 m3/s so the model could be adequately 

calibrated over the range of flow in the river; and (2) because 

MD_SWMS functions as a steady-state model, the historical 

streamflow and water-surface elevation should be stable for a 

minimum of 24 hours so river conditions approximate steady 

flow. Criterion (2) assumed that streamflow should be stable 

for a minimum of 24 hours at the Porthill stage-discharge 

gaging station (12322000) for calibration measurements prior 

to October 2002 and at the Tribal Hatchery stage-discharge 

gaging station (12310100) for calibration measurements since 

October 2002. In addition, criterion (2) assumed that watersurface elevation should be stable for a minimum of 24 hours 

at the Klockmann Ranch stage gaging station (12314000) and 

the Bonners Ferry stage gaging station (12309500). The model 

was calibrated by adjusting the drag coefficient until simulated 

water-surface slope through the modeling reach matched the 

measured water surface. Physically, this process is equivalent 

to ensuring that the roughness used in the model accurately 

simulates the head loss in the channel over long reaches. 

Figure 14. Streamflow-velocity measurements at the upstream model boundary on the white sturgeon critical-habitat reach of the 

Kootenai River at Bonners Ferry, Idaho, June 1996 and April 2002.

ID91Z00_fig14

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

0 50 100 150 200 250 300

LOCATION OF MEASUREMENT STATION AS DISTANCE FROM RIGHT BANK, IN METERS

A

VERAGE VELOCITY IN THE VERTICAL, IN METERS PER SECOND

June 7, 1996; streamflow 1,260 cubic meters

per second (44,600 cubic feet per second)

April 16, 2002: streamflow 776 cubic meters per

second (27,400 cubic feet per second)

Construction of the Multidimensional Flow Model  23
Table 2. Calibration summary for the multidimensional hydraulic flow model for the white sturgeon critical-habitat reach of the Kootenai River, near 

Bonners Ferry, Idaho.

[Method of computing stage: C, stage is based on water-surface elevation recorded at streamflow gaging stations located upstream and downstream and of the 

modeling reach; M, stage is simulated from a 1-dimensional hydraulic model. Computed Lateral Eddy Viscosity: 0.01 × average depth × average velocity. 

Abbreviations: m3/s, cubic meter per second; ft3/s, cubic foot per second; m, meter; ft, foot; m/s, meter per second; ft/s, foot per second; –, no data]

Date

Streamflow Watersurface

slope

Method of 

computing 

stage

River stage (m) River stage (ft)

Downstream 

boundary

Tribal Hatchery gage

(12310100) Upstream boundary Downstream boundary Upstream boundary

(m3/s) (ft3/s) Computed 

stage

Computed 

stage

 Model

output

Computed 

stage

 Model 

output

Computed 

stage 

Computed 

stage

Model 

output

06-23-1967 2,540 89,700 0.000042 C 541.37 – – 542.12 542.10 1,776.24 1,778.70 1,778.63

05-16-1969 2,540 89,700 .000049 C 540.62 – – 541.49 541.48 1,773.77 1,776.63 1,776.60

05-30-1969 2,270 80,200 .000040 C 540.15 – – 540.86 540.88 1,772.23 1,774.56 1,774.63

06-29-1967 1,920 67,800 .000033 C 540.07 – – 540.66 540.66 1,771.97 1,773.91 1,773.91

05-22-1969 1,660 58,615 .000036 C 538.68 – – 539.32 539.32 1,767.41 1,769.51 1,769.51

06-11-1997 1,400 49,400 .000029 C 538.17 – – 538.67 538.68 1,765.74 1,767.38 1,767.41

07-03-2002 1,340 47,300 .000032 M 537.56 – – 538.13 538.15 1,763.73 1,765.60 1,765.67

06-24-2002 1,050 37,100 .000028 C 536.89 – – 537.38 537.38 1,761.54 1,763.14 1,763.14

06-13-2003 855 30,200 .000029 M 536.21 536.56 536.55 536.73 536.71 1,759.31 1,761.01 1,760.95

12-20-2002 779 27,500 .000036 C 535.10 535.53 535.55 535.77 535.76 1,755.66 1,757.86 1,757.83

07-02-2003 592 20,900 .000025 M 535.03 535.32 535.32 535.50 535.47 1,755.43 1,756.98 1,756.88

08-13-2003 535 18,900 .000032 C 535.27 535.65 535.64 535.87 535.86 1,756.22 1,758.19 1,758.16

05-05-2003 317 11,200 .000034 C 533.02 533.33 533.34 533.67 533.66 1,748.84 1,750.97 1,750.94

11-15-2002 157 5,540 .000030 M 532.50 532.62 532.59 533.10 533.12 1,747.13 1,749.10 1,749.17

Date

Model drag coefficient 

(dimensionless)

Lateral eddy

viscosity

Average river

depth

Average streamflow

velocity

River 

kilometer 

245.8 to 

228.4

River 

kilometer 

228.4 to 

244.5

River 

kilometer 

245.8 to 

244.5

Model Computed (m) (ft) (m/s) (ft/s)

06-23-1967 0.0023 – – 0.170 0.170 14.5 47.6 1.17 3.8

05-16-1969 .0022 – – .175 .175 14.5 47.6 1.21 4.0

05-30-1969 .0018 – – .160 .161 14.0 45.9 1.15 3.8

06-29-1967 .0021 – – .145 .149 13.5 44.3 1.10 3.6

05-22-1969 .0020 – – .130 .105 11.7 38.4 .90 3.0

06-11-1997 .0020 – – .100 .092 10.6 34.8 .87 2.9

07-03-2002 .0022 – – .090 .090 10.0 32.8 .90 3.0

06-24-2002 .0026 – – .080 .076 9.5 31.2 .80 2.6

06-13-2003 .0031 – – .054 .054 8.0 26.2 .67 2.2

12-20-2002 .0032 – – .048 .048 7.4 24.3 .65 2.1

07-02-2003 .0035 – – .036 .036 6.6 21.6 .55 1.8

08-13-2003 .0043 – – .032 .028 5.6 18.4 .50 1.6

05-05-2003 .0055 – – .021 .021 5.6 18.4 .37 1.2

11-15-2002 – 0.0040 0.0150 .010 .010 4.3 14.2 .23 .8

24  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Model Boundary Conditions for Calibration Runs

Boundary conditions used during model calibration 

include (1) streamflow and water-surface elevations at the 

upstream model boundary, and (2) water-surface elevations 

at the downstream boundary. Streamflow conditions less 

than 878 m3/s were based on measurements at the Tribal 

Hatchery gaging station (1231010) for the period of record 

since October 2002 and streamflow conditions between 

878 and 2,540 m3/s were computed as streamflow at the 

Porthill gaging station (1232200) minus Boundary Creek 

gaging station (12321500) for May 23, 1967, to July 3, 2002. 

Fourteen boundary conditions for water-surface elevation at 

the downstream model boundary (table 2) were determined 

for the calibration runs. Flows greater than 1,340 m3/s were 

computed by interpolation of the water-surface elevation at 

the Bonners Ferry gaging station (12309500) and Klockmann 

Ranch gaging station (12314000). Water-surface elevation 

boundary conditions for streamflows 1,340 m3/s and less were 

obtained from a steady 1-dimensional hydraulic model of 

the Kootenai River developed by Berenbrock (2005). Onedimensional model results were unavailable for higher flows, 

but the interpolation method should be adequately accurate.

Drag Coefficient

The model was calibrated by adjusting the roughness, 

as parameterized by drag coefficient, until the simulated 

average water-surface elevation at the upstream end of the 

model reach matched the water-surface elevation determined 

from the gaging station at Bonners Ferry. For flows during the 

Tribal hatchery (12310100) gaging station operation, modeled 

water-surface elevation also was compared with measurements 

at that location (fig. 2). Because the downstream water-surface 

elevation was set as a model boundary condition, this process 

ensured that the reach-averaged water-surface slope simulated 

by the model matched the measurements. Local roughness 

values are defined primarily by grain-size distribution and, 

when bedforms are present, the amplitude and wavelength of 

the bedforms. Between Ambush Rock and Shorty Island the 

channel bottom consists of fine sand and some lacustrine clay, 

and between the U.S. Highway 95 Bridge and Ambush Rock 

the river bottom consists predominantly of gravel, cobble, 

and sand. To account for these differences the drag coefficient 

was partitioned into regions of constant drag above and below 

Ambush Rock when modeling streamflow equal to or less than 

170 m3/s. In the absence of spatially detailed measurements of 

bedforms and grain-size, a constant drag coefficient was used 

in each of these regions. 

Results

Model calibration was considered acceptable when 

the difference between model-simulated and observed 

water-surface elevations at both the Tribal Hatchery gaging 

station (12310100) and the upstream model boundary at 

Bonner’s Ferry gaging station (12309500) were minimized. 

Results of the calibration are presented in table 2. Differences 

in model-simulated and observed water-surface elevations at 

both gaging stations were less than or equal to ±0.03 m. Data 

from the Tribal Hatchery gaging station showed that, for the 

low-flow calibration streamflow of 157 m3/s, partitioning 

the drag coefficient into regions of constant drag above and 

below Ambush Rock significantly improved the comparison of 

model to the measurements. 

Model calibration (fig. 15) resulted in drag coefficients 

that ranged from 0.004 for low-flow conditions of 157 m3/s to 

0.0023 for pre-dam high-flow conditions of 2,540 m3/s. The 

drag coefficient for the sandy reach between Ambush Rock 

and Shorty Island increased sharply, from 0.004 to 0.006, as 

streamflow increased from 157 to 317 m3/s. For the straight 

reach between the U.S. Highway 95 Bridge and Ambush 

Rock, the drag coefficient decreased sharply from 0.015 to 

0.0055 as flow increased from 157 to 317 m3/s. For flows 

greater than 157 m3/s, there was no clear justification for using 

more than a single value of the drag coefficient, because model 

results were not significantly better than results obtained using 

a single value. At greater streamflows, the drag coefficient 

was constant throughout the model, decreasing gradually 

from 0.0055 to 0.0022 as streamflow increased from 317 

to 1,340 m3/s, then remaining about constant as streamflow 

increased to 2,540 m3/s. Model calibration suggests that 

bedforms have a large effect on the drag coefficient at 

streamflows less than about 595 m3/s: friction along the 

riverbed is increased at low streamflows due to formation 

of tall dunes, and friction decreases at higher streamflows 

because the dunes tend to wash out. 

The model incorporates a lateral eddy viscosity to 

represent lateral momentum exchange due to turbulence or 

other variability that is not generated at the bed (see Nelson, 

2003). The model’s lateral eddy viscosity (LEV) parameter 

was computed for each model calibration condition using 

equation (1) defined as:

LEV u y = * 0 01 avg a * vg . , (1)

where

LEV is lateral eddy-viscosity coefficient, in square 

meters per second,

is average velocity, in meters per second, and

is average depth, in meters.

The computed LEV value was applied uniformly throughout 

the modeling reach for each calibration streamflow. LEV

consistently increased with increasing streamflow (fig. 15) and 

ranged from 0.010 to 0.175 for streamflow ranging from 157 

to 2,540 m3/s.

uavg

yavg

Construction of the Multidimensional Flow Model  25
Model Validation

The model was validated by comparing simulated flow 

velocities with flow velocities measured at 15 cross sections 

between RKM 229.1 and 236.9 during steady streamflow 

that averaged 538 m3/s on August 12-14, 2003 (figs. 9 and 

16). Flow velocities were measured by an ADCP that was 

interfaced with a Trimble mapping-grade GPS receiver and 

Fugawi navigational software (http://www.fugawi.com/docs/

navframe.html). The 15 river cross sections were measured 

multiple (7-13) times to obtain average velocities suitable 

for comparison to the model results. Measured data were 

processed into cross sections of vertically averaged velocity 

and vertical distributions of velocity (vertical slice) to test 

the 2- and 2.5-dimensional model components, respectively. 

Procedures for processing raw ADCP data are described in 

general form by Dinehart (2003) and in Appendix A. 

The model simulates both the magnitude and structure of 

flow across the section reasonably well (fig. 17), with a few 

notable exceptions. The model slightly under-simulated the 

magnitude and location of peak velocities in cross sections 

at the apex of bends in the river, as in Section 2344. This is a 

common result for models that are not fully 3-dimensional, 

and can be attributed to the lack of secondary flow feedback 

on primary velocity distribution. 

Streamflow simulations for the first two sections in 

the main channel around Shorty Island (2313 and 2310) are 

notably poor. One possible explanation is that specifying 

a constant drag coefficient is inappropriate in this reach. 

Bedforms in the straight, somewhat shallow reach just 

upstream of Shorty Island likely exert a drag on flow and 

effectively steer and magnify the flow near the right side of the 

channel looking downstream, as shown in Section 2313. To 

investigate this possibility, a hyperbolic tangent function was 

used to create a smooth transition from one value to another 

(fig. 18). Using this function resulted in a smooth variation in 

drag coefficient from 0.015 at the shallowest depths to 0.001 

at depths greater than 10 m. The smooth roughness transition 

crudely simulates dunes about 2 m high in water less than 5 m 

deep and decrease in height until they are nonexistent in water 

greater than about 10 m deep. The hyperbolic tangent function 

was used only to illustrate the potential importance of dunes 

in setting the drag coefficient; it was not used in the model 

for any other purpose. A comparison of measured velocities 

with velocities simulated using a constant drag coefficient 

and a variable drag coefficient suggest that the model results 

could be improved through better understanding of the spatial 

distribution of dunes and their sizes (fig. 19). 

Figure 15. Drag and lateral eddy-viscosity coefficients for the calibrated multidimensional flow model of the white 

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho.

ID91Z00_fig15

0.0000

0.0020

0.0040

0.0060

0.0080

0.0100

0.0120

0.0140

0.0160

0 200 400 600 800 1,000 1,200 1,400 1,600 1,800 2,000 2,200 2,400 2,600 2,800

STREAMFLOW, IN CUBIC METERS PER SECOND

DRAG COEFFICIENT, DIMENSIONLESS

0.000

0.020

0.040

0.060

0.080

0.100

0.120

0.140

0.160

0.180

0.200

LATERAL EDDY VISCOSITY, DIMENSIONLESS

DRAG COEFFICIENT IN THE MEANDERING REACH FOR STREAMFLOW OF 157 CUBIC METERS

PER SECOND

DRAG COEFFICIENT IN THE STRAIGHT REACH FOR A STREAMFLOW OF 157 CUBIC- METERS PER SECOND AND FOR THE ENTIRE MODEL REACH FOR STREAMFLOW

GREATER THAN 157 CUBIC METERS PER SECOND

LATERAL EDDY VISCOSITY

26  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Figure 16. Location of acoustic Doppler current profiler cross sections for validating the multidimensional flow model for the 

white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho.

ID91Z00_fig.16

2

95

95

2

Burlington

Northern

Santa Fe

Railroad

Union

Pacific

Railroad

Pacific

Union

Railroad

BNSF Railroad

River

IDAHO

Bonners

Ferry

Deep

Creek

Myrtle Creek

Shorty

Island

Lost Creek

Ball

Creek

Ambush

Rock

Mission

Hill

C A S C A D E R A N G E

Kootenai

K O O T E N A I F L A T S

K O O T

E N A I F L A T S

Downstream

boundary for

multidimensional

model

Upstream

boundary for

multidimensional

model

12310100

12309500

12314000 Kilometer 225

Kilometer 230

Kilometer 235

Kilometer 240

Kilometer 245

Kilometer 250

2291

2306

2310

2303

2313

2326

2337 2342

2344

2345 2356 2351 2370

2366 2359

2369

116° 25' 116° 20'

48°

45'

48°

40'

EXPLANATION

AREA ABOVE FLOOD PLAIN

WHITE STURGEON CRITICAL HABITAT REACH —

 River kilometer 228 to 246

RIVER KILOMETER

ACOUSTIC DOPPLER CURRENT PROFILER

 CROSS SECTION AND NO. —

 7 to 13 profiles collected at 

 each section, August 12-14, 2003

U.S. GEOLOGICAL SURVEY 

 GAGING STATION AND NO.

Kilometer 235

12309500

+

2310

Base from U.S. Geological Survey digital data, 1:100,000, 1983

Universal Transverse Mercator projection, Zone 13

0

0 1 2 MILES

1 2 3 4 KILOMETERS

Construction of the Multidimensional Flow Model  27
ID91Z00_fig17A

SECTION 2370 

SECTION 2369 SECTION 2366 

SECTION 2356 SECTION 2351 

SECTION 2345 SECTION 2344 

VELOCITY, IN METERS PER SECOND 

DISTANCE FROM ARBITRARY DATUM, IN METERS 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

10,200 10,250 10,300 

9,900 9,950 10,000 

11,600 11,650 11,700 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

15,950 16,000 16,050 

26,950 27,000 27,050 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

100,700 100,750 100,800 

17,450 17,500 17,550 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

100,850 

APPROXIMATE LOCATION 

RIGHT BANK 

APPROXIMATE LOCATION 

RIGHT BANK 

APPROXIMATE LOCATION 

LEFT BANK 

APPROXIMATE LOCATION 

LEFT BANK 

EXPLANATION

SIMULATED VELOCITY

Each color represents an acoustic Doppler 

current profile (ADCP) collected along the 

cross section. Each cross section was measured 

multiple (7-13) times with the ADCP.

Figure 17. Measured cross sections of vertically averaged velocities and corresponding simulated velocities on the white sturgeon 

critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, for a steady flow that averaged 538 cubic meters per second on 

August 12–14, 2003. 

(As many as 13 velocity profiles were measured at each cross section. Locations of cross sections shown in figure 16.)

28  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID91Z00_fig17B

SECTION 2342 SECTION 2337 

SECTION 2326 SECTION 2313 

SECTION 2310 SECTION 2306 

SECTION 2303 SECTION 2291 

VELOCITY, IN METERS PER SECOND

DISTANCE FROM ARBITRARY DATUM, IN METERS

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

10,200 10,250 10,300 

10,450 10,500 10,600 10,650 10,700 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

15,950 16,000 16,050 9,900 9,950 10,000 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

11,100 11,150 10,050 10,100 10,150 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

16,050 16,100 16,150 

APPROXIMATE LOCATION 

RIGHT BANK 

APPROXIMATE LOCATION 

LEFT BANK 

APPROXIMATE LOCATION 

RIGHT BANK 

APPROXIMATE LOCATION 

LEFT BANK 

Figure 17. Continued.

Construction of the Multidimensional Flow Model  29
Figure 18. Functional dependence of the drag coefficient on depth, 

used to improve simulated vertically averaged velocity at cross 

section 2313 on the Kootenai River near Bonners Ferry, Idaho. 

The function uses a hyperbolic tangent to vary the drag coefficient 

smoothly from 0.015 at shallow depths to 0.001 at depths greater 

than 10 meters. The function is shown in the inset, along with the 

values used for each parameter.

ID91Z00_fig18 DRAG COEFFICIENT

DEPTH, IN METERS

0 5 10 15 20

0.015

0.010

0.005

0

Drag

coefficient

A = amplitude, 0.014

x = depth

x0 = a shift, 5

x* = how quickly the

 value changes, 2

min = minimum, 0.001

Cd= — 1-tanh +min A

2

(x-x0)

x*

SECTION 2313

with constant drag coefficient

SECTION 2313

with variable drag coefficient

VELOCITY, IN METERS PER SECOND

DISTANCE FROM ARBITRARY DATUM, IN METERS

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

9,900 9,950 10,000 9,900 9,950 10,000

EXPLANATION

APPROXIMATE LOCATION

RIGHT BANK

APPROXIMATE LOCATION

LEFT BANK

APPROXIMATE LOCATION

RIGHT BANK

APPROXIMATE LOCATION

LEFT BANK

SIMULATED VELOCITY

Each color represents an acoustic Doppler 

current profile (ADCP) collected along the 

cross section. Each cross section was measured 

multiple (7-13) times with the ADCP.

Figure 19. Measured vertically averaged velocity and simulated vertical velocity based on a constant drag coefficient and variable 

drag coefficient for cross-section 2313 on the white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, for a 

steady flow that averaged 538 cubic meters per second on August 12–14, 2003.

(Location of cross section shown in figure 16.)

30 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Validation of the model also included comparing 

measured and simulated vertical structure of downstream and 

cross-stream velocities for the 15 cross sections. Measured 

and simulated vertical structures for section 2370 are provided 

as an example (fig. 20). Downstream velocity is the flow 

component perpendicular to the measured cross section and 

cross-stream velocity is the flow component parallel to the 

measured section. These profiles were assembled by first 

straightening each measured cross section, as described in 

Dinehart and Burau (2003; in press). The ensemble-averaged 

velocity structure then was obtained by interpolating all 

measured cross sections onto a vertical grid spanning the 

channel and oriented, as nearly as possible, perpendicular 

to mean flow direction. Measuring velocities in a large 

number of ADCP cross sections was intended to increase 

the possibility that the velocity structure represents average 

flow. The fact that the contours for measured velocity show 

extensive variability compared to those of simulated velocity 

(fig. 20) reflects, in part, both the natural variability of flow 

due to turbulence and smaller scale features that cannot be 

resolved by the model and the possibility that the number 

of measured profiles was inadequate for obtaining a true 

average. The differences in topography between the measured 

section and the modeled section are due to: local variation in 

topography, the presence of dunes, some smoothing of the 

banks due to discretization of the topography, and the fact that 

modeled topography was measured at a different time than 

the topography determined from the ADCP measurements. 

Differences in depths are as much as 2 m, which is consistent 

with the dune amplitudes, and differences in width are on the 

order of 5 m, which is comparable to the grid spacing.

For downstream and cross-stream velocity, the 

streamflow simulations represent both the magnitudes and 

structure of flow reasonably well, including the position of 

the velocity maxima and the strength of the cross-stream 

flow (fig. 20). Similar results are found for all cross sections, 

with the exception of sections 2313 and 2310, as discussed 

previously. 

Model Sensitivity Analysis

Sensitivity analysis of the model consisted of decreasing 

and increasing the calibrated drag coefficient by 75 and 125 

percent during streamflow simulation runs of 170, 566, 1,130, 

1,700, and 2,270 m3/s. The analysis includes reporting median 

and maximum river water-surface elevation, velocity, and 

boundary shear stress for the entire population of wet model 

nodes (table 3). Varying calibrated drag coefficient by 75 

and 125 percent changed the median water-surface elevation 

on average by 0.05 m. Model-simulated velocities were not 

sensitive to the choice of drag coefficient. Model-simulated 

shear stress changed proportionally with the drag coefficient. 

The sensitivity analysis highlights the importance of first 

calibrating the model to the roughness, mainly to accurately 

simulate shear stress. 

Construction of the Multidimensional Flow Model  31
Figure 20. Measured and simulated vertical profiles of downstream velocity and cross-stream velocity at section 2370 on the white 

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, for a steady flow that averaged 538 cubic meters per 

second on August 12–14, 2003.

(Location of cross section shown in figure 17.)

ID 91Z00_fig20aARBITRARY ELEVATION, IN METERS

ARBITRARY DISTANCE FROM FROM LEFT BANK, IN METERS

ELEVATION, IN METERS

15

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

-10 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150

537

536

535

534

533

532

531

530

529

528

527

526

525

524

523

522

MEASURED

SIMULATED

A. DOWNSTREAM VELOCITY

0 to 0.2

0.2 to 0.4

0.4 to 0.6

0.6 to 0.8

Greater than

 0.8

Velocity, in meters

per second

32  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID91Z00_fig 20bARBITRARY ELEVATION, IN METERS

ARBITRARY DISTANCE FROM FROM LEFT BANK, IN METERS

ELEVATION, IN METERS

15

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

-10 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150

537

536

535

534

533

532

531

530

529

528

527

526

525

524

523

522

MEASURED

SIMULATED

B. CROSS-STREAM VELOCITY

Greater than

 0.3

Velocity, in meters

per second

-0.3

-2.0

-1.0

0. 

0.1

0.2

-2.0

-1.0

 0

 0.1

 0.2

 0.3

to

to

to

to

to

to

Figure 20. Continued.

Construction of the Multidimensional Flow Model  33
Simulation of Flow and Sediment 

Mobility in the White Sturgeon 

Critical-Habitat Reach

The model was used to simulate water-surface elevation, 

depth, velocity, bed shear stress, and sediment mobility 

in the Kootenai River for streamflows of 170, 566, 1,130, 

1,700, and 2,270 m3/s. The range of simulated streamflows 

was selected to span river conditions typical of those before 

and since the construction of Libby Dam. The three lowest 

streamflows represent a range of conditions that have occurred 

throughout the historical record. The highest streamflow 

(2,270 m3/s) represents a discharge that is approximately equal 

to the annual median peak streamflow (2,237 m3/s) prior to 

emplacement of Libby Dam in 1972. Streamflows greater than 

566 m3/s were increased incrementally by 570 m3/s.

For each of the five streamflows simulated using the 

model, it was necessary to set a boundary condition for 

water-surface elevation at the lower end of the modeled reach 

(table 4). This was determined by searching the historical 

record of mean daily streamflow for periods when the 

streamflow of interest was approximately steady for a few 

days. The 170 m3/s and 566 m3/s streamflows were based on 

the 2002-03 record from the Tribal Hatchery gaging station 

(12310100) in the model reach. The 1,130 , 1,700, and 

2,270 m3/s streamflows were based on the pre-Libby Dam era, 

when streamflow was much higher. Mean daily streamflow for 

the modeled reach was calculated as that at the Porthill gaging 

station (12322000) minus tributary inflow from Boundary 

Creek gaging station (12321500) during the pre Libby-dam era 

between 1965 and 1971. The Klockmann Ranch gaging station 

(12314000) and the Bonners Ferry gaging station (12309500) 

have no water-surface elevation-discharge relation. 

Table 3. Sensitivity analysis and results of the multidimensional flow model for the white sturgeon critical-habitat reach of the Kootenai River near 

Bonners Ferry, Idaho, for five streamflows.

[Streamflow for river model simulation: The model is constructed with a variable drag coefficient for the 170-cubic-meter-per-second flow-management 

scenario: a drag coefficient of 0.015 is specified for the reach between the model’s upstream boundary and Ambush Rock, and 0.004 is specified for the reach 

between Ambush Rock and the model’s downstream boundary. Sensitivity analyses of the calibrated drag coefficient were made at 75 and 125 percent of the 

drag coefficient value. Reported median and maximum values are based on the population of all wet nodes in the model. Abbreviations: m3/s, cubic meter per 

second; ft3/s, cubic foot per second; m, meter; ft, foot; Med., median; Max., maximum; m/s, meter per second; ft/s, foot per second; newtons/m2, newtons per 

square meter]

Streamflow for river 

model simulation Drag

coefficient

value

Depth Velocity Shear stress

(newtons/m2)

Water-surface elevation

(m) (ft) (m/s) (ft/s) (m) (ft)

(m3/s) (ft3/s) Med. Max. Med. Max. Med. Max. Med. Max. Med. Max. Med. Max. Med. Max.

170 6,000 0.0040

 .0150

4.46 19.98 14.63 65.55 0.25 1.07 0.82 3.51 0.25 19.05 533.18 533.54 1,749.36 1,750.54

.0030 

 .0113

4.45 19.97 14.60 65.52 .19 1.30 .62 4.27 .19 17.05 533.18 533.49 1,749.36 1,750.38

.0050

 .0188

4.46 20.00 14.63 65.62 .31 1.09 1.02 3.58 .31 22.50 533.19 533.59 1,749.40 1,750.71

566 20,000 .00400 6.14 22.08 20.15 72.44 .57 1.20 1.87 3.94 1.28 5.80 534.99 535.30 1,755.30 1,756.32

.00300 6.10 22.01 20.01 72.21 .57 1.30 1.87 4.27 .98 5.10 534.95 535.21 1,755.17 1,756.02

.00500 6.17 22.16 20.24 72.71 .56 1.19 1.84 3.90 1.58 7.02 535.03 535.38 1,755.43 1,756.58

1,130 40,000 .00260 7.97 24.39 26.15 80.02 .79 1.41 2.59 4.63 1.65 5.18 537.25 537.61 1,762.72 1,763.90

.00195 7.94 24.32 26.05 79.79 .80 1.43 2.62 4.69 .82 4.74 537.21 537.54 1,762.59 1,763.67

.00325 8.00 24.46 26.25 80.25 .79 1.37 2.59 4.50 2.03 6.07 537.29 537.69 1,762.85 1,764.16

1,700 60,000 .00200 9.33 26.10 30.61 85.63 .95 1.53 3.12 5.02 1.80 4.68 538.95 539.39 1,768.30 1,769.74

.00150 9.31 26.08 30.55 85.57 .95 1.56 3.12 5.12 1.34 3.66 538.92 539.34 1,768.20 1,769.57

.00300 9.37 26.23 30.74 86.06 .94 1.49 3.08 4.89 2.63 7.59 539.01 539.50 1,768.49 1,770.10

2,270 80,000 .00200 10.43 27.76 34.22 91.08 1.03 1.80 3.38 5.91 2.16 6.48 540.53 540.97 1,773.48 1,774.92

.00150 10.40 27.64 34.12 90.69 1.00 1.84 3.28 6.04 1.52 5.06 540.50 540.89 1,773.38 1,774.66

.00250 10.47 27.85 34.35 91.38 1.04 1.77 3.41 5.81 2.68 7.83 540.58 541.07 1,773.64 1,775.25

34  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
As noted in the discussion of downstream water-surface 

elevation conditions for the calibration runs, water-surface 

elevation at the downstream model boundary for each 

streamflow simulated with the model is a linear interpolation 

of the water-surface elevation as recorded at the Bonners 

Ferry gaging station and the Klockmann Ranch gaging station 

(12314000). For each of the streamflows, 10-17 periods of 

approximately steady mean daily streamflow were identified 

and the water-surface elevation at the downstream model 

boundary was interpolated for each period. The watersurface elevation boundary condition then was identified as 

the median of all the calculated values. Table 4 presents the 

median, minimum, and maximum mean daily streamflow and 

water-surface elevation boundary condition for each of the five 

simulations. 

Modeling results for the five streamflows provide insight 

into the spatial variability of water-surface elevation, depth, 

velocity, and shear stress (table 3). Median and maximum 

river depth, velocity, and shear stress are computed for all wet 

nodes in the model for each of the five simulated streamflows. 

In addition, for each of the five simulated streamflows, the 

average, maximum, and standard deviation of water-surface 

elevation, depth, velocity, and sediment mobility were 

calculated at 174 cross sections of the river channel, positioned 

every 100 m along the length of the model reach. 

A few simple simulations are presented below to 

demonstrate how the model can be used to link physical 

characteristics of streamflow to biological or other habitat 

data. Some measures of depth, velocity, and substrate 

composition generally are considered when assessing sturgeon 

spawning habitat (Parsley and others, 1993). Habitat suitability 

curves developed for white sturgeon in the Lower Columbia 

River (Parsley and Beckman, 1994) were used to characterize 

conditions in the Kootenai River spawning habitat. 

Requirements for Kootenai River white sturgeon spawning 

habitat may vary from that in the Lower Columbia River; 

however, both rivers are highly-regulated systems. Discussions 

of the model simulation include relating the model results to 

observed patterns of spawning and egg locations, specifically 

Streamflow 

for model 

simulations

Streamflow at upstream model boundary Water-surface elevation at downstream model boundary

Median Minimum Maximum Median Minimum Maximum

(m3/s) (ft3/s) (m3/s) (ft3/s) (m3/s) (ft3/s) (m3/s) (ft3/s) (m) (ft) (m) (ft) (m) (ft)

170 6,000 170 6,006 163 5,750 178 6,280 532.97 1,748.59 532.50 1,747.05 533.38 1,749.93

566 20,000 547 19,300 535 18,900 592 20,900 534.71 1,754.30 534.27 1,752.85 535.03 1,755.35

1,130 40,000 1,130 40,000 1,120 39,500 1,145 40,400 536.98 1,761.75 536.06 1,758.73 538.02 1,765.16

1,700 60,000 1,710 60,300 1,680 59,200 1,719 60,700 538.65 1,767.22 538.65 1,767.22 539.48 1,769.95

2,270 80,000 2,270 80,000 2,250 79,300 2,285 80,700 540.22 1,772.38 539.50 1,770.01 540.92 1,774.67

Table 4. Upstream and downstream boundary conditions in the multidimensional flow model for the white sturgeon critical-habitat reach of the 

Kootenai River near Bonners Ferry, Idaho.

[Streamflow at upper model boundary: Computed as streamflow at Porthill gaging station (12322000) minus streamflow at Boundary Creek gaging station 

(12321500). Abbreviations: m3/s, cubic meter per second; ft3/s, cubic foot per second; m, meter; ft, foot]

the number of spawning events per unit of effort (SEPUE), to 

illustrate how model results can be combined with biological 

data or other assessments of habitat quality.

Water-Surface Elevation Profiles and 

Free-Flowing and Backwater Streamflow

The modeling results do not support the hypothesis 

presented by Paragamian and others (2001) that the relative 

location of free-flowing and backwater streamflow may 

play a role in influencing white sturgeon spawning patterns. 

In view of this hypothesis, simulation of the water-surface 

elevation profiles over a range of streamflows is important. 

Model results for the five simulated streamflows and spawning 

event locations are presented here. Water-surface elevations 

vary by about 7 m between the lowest and highest streamflow 

simulations. Average slope of the water surface increased 

as streamflow increased (fig. 21), with slopes from lowest 

to highest simulated streamflow of 0.000014, 0.000028, 

0.000033, 0.000037, and 0.000041 m3/s, respectively. The 

170-m3/s streamflow simulation has the gentlest slope for 

the entire modeling reach; however, the slope of the water 

surface is markedly steeper (0.0002) than slopes associated 

with streamflow simulations over a 600-m reach downstream 

of the U.S. Highway 95 Bridge between RKM 245.4 and 246. 

The greater slope indicates water is free flowing in this short 

reach for this low streamflow; whereas, backwater conditions 

exist for the four larger streamflows. This occurs because 

water levels in Kootenay Lake tend to be low during periods of 

low streamflow and high during periods of higher streamflow. 

Since 1994, white sturgeon spawning was detected at egg-mat 

monitoring stations only in 2001, at RKM 245.7 and 245.1, 

in the straight reach between Ambush Rock and the U.S. 

Highway 95 Bridge (Paragamian and others, 2002). During 

2001, spawning occurred further upstream than any other time 

during 1994-2001, at the same time, free-flowing streamflow 

was further downstream than any other spawning event during 

the same period. These spawning events occurred during flows 

between 179 and 188 m3/s, which are similar to the 170-m3/s 

streamflow simulation. 

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  35
River Depth

The model simulated median and maximum river 

depth for all wet nodes (table 3). For the lowest and highest 

streamflow simulations (170 and 2,270 m3/s) these variables 

ranged from 4.5 to 10.4 m and from 20.0 to 27.8 m, 

respectively. The model also simulated average and maximum 

water depth for the five streamflows at cross sections every 

100 m along the modeled reach (fig. 22). The river depth 

is shallowest in the upper one-half kilometer or so of the 

straight reach. In this area, the average depth for the lowest 

and highest streamflow simulations is 2.5 and 8.7 m and the 

maximum depth is 4.3 and 12.0 m. Below Ambush Rock, in 

the meandering reach, the average depth is 6.8 and 14.6 m and 

the maximum river depth is 15.6 and 23.1 m. 

The river channel is locally deep in several areas along 

the model reach (fig. 22). The deepest point in the channel is 

at Ambush Rock, where the maximum river depth is 19.8 m 

for the lowest simulated flow and 27.5 m for the highest 

simulated flow. Other deep areas are at the outside of the 

channel where the channel curvature is highest in the S-shaped 

meander near Myrtle Creek. The deep area near RKM 240.6 

is associated with a bedrock outcrop on the left bank just 

upstream of the mouth of Deep Creek. A lateral recirculation 

eddy forms downstream of the outcrop and a deep hole with 

a depth ranging from 10.2 to 17.9 m is in the main channel 

adjacent to the eddy. Another deep hole is associated with a 

lateral recirculation eddy at RKM 229.8, along the right bank 

near the downstream end of Shorty Island, with a maximum 

depth of 13.6 to 20.9 m. 

Egg collection on the Kootenai River during the past 12 

spawning seasons shows that sturgeon eggs tend to accumulate 

in the thalweg, where depths can exceed 14 m (Vaughn 

Paragamian, U.S. Fish and Wildlife Service, oral commun., 

2005). Parsley and Beckman (1994) presented microhabitat 

criteria curves showing that the depths for spawning white 

sturgeon in the Lower Columbia River range from 3.5 to 

25 m. Habitat suitability in the straight reach ranges from 

poor to excellent and in the meandering reach is generally 

excellent (fig. 22). Although a comparison of simulated 

ID91Z00_fig21

2,270 cubic meters per second (80,000 cubic feet per second)

1,700 cubic meters per second (60,000 cubic feet per second)

566 cubic meters per second (20,000 cubic feet per second)

1,130 cubic meters per second (40,000 cubic feet per second)

170 cubic meters per second (6,000 cubic feet per second)

STURGEON SPAWNING EVENTS PER UNIT OF EFFORT (SEPUE) DURING 1994-2001

0

20

40

SEPUE X

10,000 540.0

540.2

540.4

540.6

540.8

541.0

538.6

538.8

539.0

539.2

539.4

534.6

534.8

535.0

535.2

535.4

536.8

537.0

537.2

537.4

537.6

532.8

532.9

533.0

533.1

533.2

W

ATER SURFACE ELEV

ATION, IN METERS

 Meander 

reach

Straight

reach

DEEP

CREEK

MYRTLE

CREEK SHORTY ISLAND

AMBUSH

ROCK

River Kilometers 229.6 - 231.45 River Kilometer 234.63 River Kilometer 240.25 River Kilometers 244.1 - 244.6

228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246

DISTANCE, IN RIVER KILOMETERS

Figure 21. Simulated average water-surface elevation for five streamflows at cross sections positioned every 100 meters along the 

white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and spawning event locations.

36  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
river depth and sturgeon spawning event locations per unit 

effort (egg locations) in the critical-habitat reach indicate 

that egg locations are preferentially found in deeper areas 

(fig. 22), careful analysis suggests that this is only a weak 

positive correlation (McDonald and others, 2004). Eggs are 

only slightly more likely to be found in deeper parts of the 

river. This correlation becomes slightly stronger if simulation 

results upstream of Ambush Rock (in the straight reach) are 

neglected. 

Streamflow Velocity

The model simulates both streamwise and cross-stream 

velocity components at 15 points in the vertical for every 

horizontal grid point in the model reach, so providing a 

simple synopsis of all the information is difficult. However, 

a general description of the river velocity structure can be 

developed by examining variation of median and maximum 

values of simulated velocity for all model nodes (table 3), as 

was done for the discussion of flow depth. The model also 

simulated average and maximum velocity for cross-sections 

located every 100 m along the model reach (fig. 23). Median 

and maximum velocity ranged from 0.25 and 1.07 m/s for 

the lowest streamflow to 1.0 and 1.8 m/s for the highest 

streamflow (table 3). The spatial variation in velocity across 

the river channel has been quantified using the standard 

deviation of velocity at cross sections positioned every 100 m 

along the length of the model reach. Standard deviation of 

velocity increases more than four-fold as streamflow increases 

from the lowest to the highest streamflow simulations (fig. 24), 

from an average of 0.09 to 0.43 m/s for the streamflow 

simulation of 170 and 2,270 m3/s.

Figure 22. Simulated average and maximum depth for five streamflows at cross sections positioned every 100 meters along the white 

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and spawning event locations.

Spawning habitat suitability were developed for the white sturgeon in the Lower Columbia River (Parsley and Beckman, 1994). Requirements 

for Kootenai River white sturgeon spawning habitat may vary from that of the Lower Columbia River.

ID 9J002_fig22

EXPLANATION

Average, 170 cubic meters per second (6,000 cubic feet per second) Maximum, 170 cubic meters per second (6,000 cubic feet per second)

Average, 566 cubic meters per second (20,000 cubic feet per second) Maximum, 566 cubic meters per second (20,000 cubic feet per second)

Average, 1,130 cubic meters per second (40,000 cubic feet per second) Maximum, 1,130 cubic meters per second (40,000 cubic feet per second)

Average, 1,700 cubic meters per second (60,000 cubic feet per second) Maximum, 1,700 cubic meters per second (60,000 cubic feet per second)

Average, 2,270 cubic meters per second (80,000 cubic feet per second) Maximum, 2,270 cubic meters per second (80,000 cubic feet per second)

EXCELLENT HABITAT SUITABILITY

Ambush

Rock

228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246

DISTANCE, IN RIVER KILOMETERS

0

2

4

6

8

10

12

14

16

18

20

22

24

26

28

DEPTH, IN METERS

0

10

20

30

40

SEPUE X 10,000

DEEP

CREEK

MYRTLE

SHORTY ISLAND CREEK

AMBUSH

ROCK

River Kilometers 229.6 - 231.45 River Kilometer 234.63 River Kilometer 240.25 River Kilometers 244.1 - 244.6

Meander

reach reach

Straight

STURGEON SPAWNING PER UNIT OF EFFORT (SEPUE) DURING 1994-2001

MODERATE HABITAT SUITABILITY

POOR HABITAT SUITABILITY

Straight or gently curved

reach (no line represents

reach with high curvature)

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  37
The model reach can be divided into three velocity zones 

on the basis of the difference and variability of maximum 

simulated velocity along the length of the model reach 

(fig. 23). Zone A, between the upstream model boundary 

and Ambush Rock, is a region of high velocity. Maximum 

velocities in zone A generally are higher than those in the 

rest of the model reach, but the differences decrease with 

increasing streamflow (fig. 24). Zone B, between Ambush 

Rock and the first sharp meander below the mouth of 

Deep Creek at RKM 237.5, has less variable maximum 

streamflow velocities compared to the rest of the model 

reach. One notable exception is near the deep hole and lateral 

recirculation eddy above Deep Creek mentioned earlier. Zone 

C, downstream of zone B and extending to the downstream 

model boundary at RKM 228.4, shows variations in the 

maximum velocity that increase with increasing streamflow. 

The greatest variability in velocity shown by the standard 

deviation (fig. 24) is a reflection of the complex channel 

geometry through the S-shaped meander and flow divergence 

around Shorty Island. The greatest occurrence of white 

sturgeon spawning is in zone C (fig. 24). 

Studies on the Columbia River indicate that sturgeon 

seek areas of high velocity for spawning (Parsley and others, 

1993). In other studies, lake sturgeon were found to spawn 

in tributary rapids (Auer, 1996; LaHaye and others, 1992). 

Spawning habitat suitability for streamflow velocity in the 

model is evaluated here using the research of Parsley and 

Beckman (1994). In the meander reach, the average velocity 

ID91Z00_fig23

EXPLANATION

Average, 170 cubic meters per second (6,000 cubic feet per second) Maximum, 170 cubic meters per second (6,000 cubic feet per second)

Average, 566 cubic meters per second (20,000 cubic feet per second) Maximum, 566 cubic meters per second (20,000 cubic feet per second)

Average, 1,130 cubic meters per second (40,000 cubic feet per second) Maximum, 1,130 cubic meters per second (40,000 cubic feet per second)

Average, 1,700 cubic meters per second (60,000 cubic feet per second) Maximum, 1,700 cubic meters per second (60,000 cubic feet per second)

Average, 2,270 cubic meters per second (80,000 cubic feet per second) Maximum, 2,270 cubic meters per second (80,000 cubic feet per second)

MODERATE HABITAT SUITABILITY

POOR HABITAT SUITABILITY

Zone A

Zone C Zone B

DEEP

CREEK

MYRTLE

SHORTY ISLAND CREEK

AMBUSH

ROCK

River Kilometers 229.6 - 231.45 River Kilometer 234.63 River Kilometer 240.25 River Kilometers 244.1 - 244.6

Meander

reach Straight

reach

STURGEON SPAWNING EVENTS PER UNIT OF EFFORT (SEPUE) DURING 1994-2001

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246

VELOCITY, IN METERS PER SECOND

0

20

40

SEPUE X 10,000

DISTANCE, IN RIVER KILOMETERS

Figure 23. Simulated average and maximum velocity for five streamflows at cross sections positioned every 100 meters along the white 

sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and spawning event locations. 

Spawning habitat suitability were developed for the white sturgeon in the Lower Columbia River (Parsley and Beckman, 1994). 

Requirements for Kootenai River white sturgeon spawning habitat may vary from that of the Lower Columbia River.

38  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
at streamflows of 1,700 and 2,270 m3/s is classified moderate 

except for parts of the reach at Shorty Island, where velocity 

is classified poor; streamflows of 1,130 m3/s and less are 

classified poor. In the straight reach, the average velocity 

at all streamflows is classified poor to moderate except at a 

streamflow of 170 m3/s, which is classified poor throughout 

the reach (fig. 23).

Streamflow velocities equal to or greater than 1.0 m/s 

are believed to greatly reduce or eliminate predation of white 

sturgeon eggs (Bob Hallock, U.S. Fish and Wildlife Service, 

oral commun., 2005) and based on the modeling results, 

the velocities seldom are equal or greater than 1.0 m/s. The 

simulated average velocity in the main channel at Shorty Island, 

where white sturgeon most frequently spawn (Paragamian and 

others, 2002), does not approach 1.0 m/s until streamflow is 

2,270 m3/s, and this only occurs near RKM 231.1 (figs. 23 and 

25). Streamflow of this magnitude only occurred prior to the 

Libby Dam era. However, maximum simulated velocity in the 

spawning reach is greater than 1.0 m/s for flows equal to and 

greater than a streamflow of 1,130 m3/s. During the Libby 

Dam era there have been very few spawning seasons with 

streamflow of 1,130 m3/s or greater.

Figure 24. Standard deviation of simulated velocity for five streamflows at cross sections positioned every 100 meters along the 

white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and spawning event locations.

ID91Z00_fig24

170 cubic meters per second (6,000 cubic feet per second)

566 cubic meters per second (20,000 cubic feet per second)

1,130 cubic meters per second (40,000 cubic feet per second)

1,700 cubic meters per second (60,000 cubic feet per second)

2,270 cubic meters per second (80,000 cubic feet per second)

EXPLANATION

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246

DISTANCE, IN RIVER KILOMETERS

STANDARD DEVIATION OF VELOCITY, IN METERS PER SECOND

DEEP

CREEK

MYRTLE

SHORTY ISLAND CREEK

AMBUSH

ROCK

Meander reach Straight

reach

River Kilometers 229.6 - 231.45 River Kilometer 234.63 River Kilometer 240.25 River Kilometers 244.1 - 244.6

STURGEON SPAWNING EVENTS PER UNIT OF EFFORT (SEPUE) DURING 1994-2001

20

40

SEPUE X

10,000

0

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  39
ID 91Z00_fig25A

1.79

1.67

1.55

1.43

1.31

1.19

1.07

0.93

0.83

0.71

0.60

0.48

0.36

0.24

0.17

0.00

A. SIMULATED STEAMFLOW, 170 CUBIC METERS PER SECOND.

B. SIMULATED STEAMFLOW, 566 CUBIC METERS PER SECOND.

METERS PER SECOND

SIMULATED VELOCITY STRUCTURE IS CONTINUED DOWNSTREAM ON THE OPPOSING PAGE.

Kootenai River

Kootenai River

Bonners Ferry

Bonners Ferry

UPSTREAM

MODEL

BOUNDARY

UPSTREAM

MODEL

BOUNDARY

Figure 25. Distribution of simulated velocity for five streamflows in the white sturgeon critical-habitat reach of the 

Kootenai River near Bonners Ferry, Idaho.

(Showing velocity at the same scale for all river-management scenarios for the sake of comparison means that some detail is 

lost for the lower streamflow scenarios.)

40 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID 91Z00_fig25B

1.79

1.67

1.55

1.43

1.31

1.19

1.07

0.93

0.83

0.71

0.60

0.48

0.36

0.24

0.17

0.00

A. SIMULATED STREAMFLOW, 170 CUBIC METERS 

 PER SECOND.—Continued

B. SIMULATED STREAMFLOW, 566 CUBIC METERS 

 PER SECOND.—Continued

METERS PER SECOND

Kootenai River Kootenai River

Shorty

Island

Shorty

Island

DOWNSTREAM

MODEL

BOUNDARY

DOWNSTREAM

MODEL

BOUNDARY

Figure 25. Continued.

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  41
ID 91Z00_fig25C

1.79

1.67

1.55

1.43

1.31

1.19

1.07

0.93

0.83

0.71

0.60

0.48

0.36

0.24

0.17

0.00

C. SIMULATED STEAMFLOW, 1,130 CUBIC METERS PER SECOND.

D. SIMULATED STEAMFLOW, 1,700 CUBIC METERS PER SECOND.

METERS PER SECOND

SIMULATED VELOCITY STRUCTURE IS CONTINUED DOWNSTREAM ON THE OPPOSING PAGE.

Kootenai River

Kootenai River

Bonners Ferry

Bonners Ferry

UPSTREAM

MODEL

BOUNDARY

UPSTREAM

MODEL

BOUNDARY

Figure 25. Continued.

42  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID 91Z00_fig25CC

1.79

1.67

1.55

1.43

1.31

1.19

1.07

0.93

0.83

0.71

0.60

0.48

0.36

0.24

0.17

0.00

C. SIMULATED STREAMFLOW, 1,130 CUBIC 

 METERS PER SECOND.—Continued

METERS PER SECOND

Kootenai River

Kootenai River

Shorty

Island

Shorty

Island

DOWNSTREAM

MODEL

BOUNDARY

DOWNSTREAM

MODEL

BOUNDARY

D. SIMULATED STREAMFLOW, 1,700 CUBIC 

 METERS PER SECOND.—Continued

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  43

Figure 25. Continued.
ID 91Z00_fig25D

1.79

1.67

1.55

1.43

1.31

1.19

1.07

0.93

0.83

0.71

0.60

0.48

0.36

0.24

0.17

0.00

E. SIMULATED STEAMFLOW, 2,270 CUBIC METERS PER SECOND.

METERS PER SECOND

SIMULATED VELOCITY STRUCTURE IS CONTINUED DOWNSTREAM ON THE OPPOSING PAGE.

Kootenai River

Bonners Ferry

UPSTREAM

MODEL

BOUNDARY

Figure 25. Continued.

44  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
ID 91Z00_fig25E

1.79

1.67

1.55

1.43

1.31

1.19

1.07

0.93

0.83

0.71

0.60

0.48

0.36

0.24

0.17

0.00

E. SIMULATED STREAMFLOW, 2,270 CUBIC 

 METERS PER SECOND.—Continued

METERS PER SECOND

Kootenai River

Shorty

Island

DOWNSTREAM

MODEL

BOUNDARY

Recently collected LIDAR data indicates the elevation of 

Shorty Island is lower than that used on the multidimentional model.

Inundation of Shorty Island may be substantially greater than 

shown in this simulation of high flow pre-Libby Dam conditions.

Figure 25. Continued.

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  45
Sediment Mobility

The model-simulated bed shear stress was used to assess 

sediment mobility over a range of streamflows from 170 to 

2,270 m3/s for several particle sizes representative of the 

meandering reach below Ambush Rock and the straight reach 

above Ambush Rock. The ability of flow to move sediment 

most often is related to the shear stress of flow at the bed. 

Sediment movement occurs at a threshold or critical shear 

stress (Julien, 2002). FaSTMECH calculates bed shear stress 

as follows:

 , (2)

where the variables are defined as follows:

Tb is boundary shear stress, in newtons per square 

meter,

r is fluid density, in kilograms per cubic meter,

Cd is non-dimensional drag coefficient,

u is vertically averaged streamwise velocity, in 

meters per second, and

v is vertically averaged cross-stream velocity, in 

meters per second.

In sand-bedded channels where bedforms are present, 

such as the Kootenai River white sturgeon critical-habitat 

reach, the total boundary shear stress needs to be partitioned 

as calculated by the flow model into a form drag component 

due to bedforms and a skin friction component due to the 

sediment surface (McLean, 1992). In other words, resistance 

to flow, or drag coefficient, is the sum of resistance due to 

bedforms when present and resistance due to sediment grains 

making up the bed. Resistance to flow due to sediment grains 

is responsible for the movement of sediment. The component 

of shear acting on the grains can be calculated from the total 

shear stress as follows (Bennett, 1995, equation 9; Smith and 

McLean, 1977; and, Nelson and others, 1993):

 t t ' / /(( / ( / l)ln ( . / )) o C K d o = + 1 1 2 0 368 z

2 2 D D , (3)

where the variables are defined as follows:

t '

o is grain shear stress,

t is total boundary shear stress, derived from 

MD_SWMS output,

Cd is drag coefficient for bedforms, typically has a 

value of 0.2,

K is von Karman’s constant,

D is bedform wavelength, user defined,

l is bedform wavelength, user defined, and

zo is roughness height, user defined.

Table 5. Sediment grade scale and critical shear stress for determining 

approximate condition for sediment mobility at 20 degrees Celsius.

[Sediment mobility for a given grain size occurs when the boundary shear 

stress exceeds the critical shear stress. It is important to note that this only 

determines whether or not a given grain size is mobile. Abbreviations: mm, 

millimeter; newtons/m2, newtons per square meter; >, greater than. Source: 

Pierre Julien (1998, table 7.1)]

Class name Diameter

(mm)

Shields critical 

shear stress

 (dimensionless)

Critical shear 

stress

(newtons/m2)

Boulder >2,048 0.054 1,790

Large >1,024 .054 895

Medium >512 .054 447

Small >256 .054 223

Cobble

Large >128 .054 111

Small >64 .052 53

Gravel

Very coarse >32 .05 26

Coarse >16 .047 12

Medium >8 .044 5.7

Fine >4 .042 2.71

Very fine >2 .039 1.26

Sand

Very coarse >1 .029 .47

Coarse >.5 .033 .27

Medium >.25 .048 .194

Fine >.125 .072 .145

Very fine >.0625 .109 .11

Silt

Coarse >.031 .165 .083

Medium >.016 .25 .065

For all flows modeled in the sand-bedded reach, the fraction 

of the total bed shear stress that is due to the grain shear stress 

was calculated and used to assess the sediment mobility. 

Critical shear stress for grain motion is based on Shields 

(1936) using equation (4).

τ γ c s = ∗ D sθ , (4)

where:

τ c is critical shear stress for grain motion, 

newtons/m2,

Ds is grain diameter, in meters,

γ s is sediment density, and

θ ∗ is dimensionless Shields parameter.

Table 5 summarizes the dimensionless Shields critical shear 

stress and critical shear stress values for a range of sediment 

sizes. Sediment mobility for a given grain size occurs when 

the boundary shear stress exceeds the critical shear stress. 

Tb = + rCd ( ) u v

2 2

46  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
This analysis determines whether or not a given grain 

size is mobile, but does not calculate potential for erosion 

or deposition, which is determined by the divergence or 

convergence in the sediment transport rate, which is not 

addressed in this report.

Grain shear stress within the straight reach was set 

equal to the total shear stress. Grain shear stress within the 

meandering reach for three of the five streamflow simulations 

was simulated by specifying a dune amplitude and bedform 

wavelength equivalent to the average dune geometry that 

was observed during 2002 (table 1). The dune amplitude and 

wavelength specified in the model for the 170-m3/s streamflow 

simulation are 0.66 m and 20.4 m, for the 566-m3/s streamflow 

simulation are 0.45 m and 18.7 m, and for the 1,130-m3/s 

streamflow simulation are 0.2 m and 13.1 m, respectively. 

For the 1,700- and 2,270-m3/s streamflow simulations the 

bedforms were assumed to have washed out, as discussed 

earlier. Calculations based on the Rouse number, which can 

be used to describe the relative importance of transport mode 

(bedload versus suspended load) suggest that at the highest 

flows the transport is dominated by suspended load transport 

and support the assumption that dunes wash out. Therefore, 

the bedform drag component of the total boundary shear 

stress is considered negligible for the highest flows, so total 

boundary shear stress is equivalent to grain shear stress.

Quantification of sediment mobility provides preliminary 

insight into streamflow requirements for flushing silt and 

sand currently burying gravel and cobble substrate that could 

be used for spawning and egg incubation. Very-fine to fine 

gravel is mobile in the straight reach for all five streamflow 

simulations; however, at the lowest streamflow of 170 m3/s 

gravel is mobile in only the upper half of the reach (fig. 26). 

Very coarse sand (b-axis diameter of >1.0 mm and <2 mm) is 

not mobile for about the lower third of the straight reach for 

the 170 m3/s streamflow simulation. Gravel becomes slightly 

more mobile at higher streamflows because the maximum 

grain shear stress increases as streamflow increases from the 

lowest to the highest streamflow simulations (fig. 26), from 

cross-sectional average values of 0.2 newtons per square 

meter (N/m2) to 5.0 N/m2 and 2.3 N/m2 to 6.2 N/m2 for the 

streamflow simulations of 170 and 2,270 m3/s, respectively. 

However, gravel is most mobile for streamflow simulation of 

170 m3/s at RKM 245.9.

In contrast to the straight reach, very fine gravel (b-axis 

diameter of >2 mm and <4 mm) is mobile in the meandering 

reach for only the three highest streamflow simulations of 

1,130, 1,700, and 2,270 m3/s. Some gravel, cobble, and riprap 

are on the riverbed in the meandering reach, as noted earlier, 

but these sediments generally are in limited areas along the 

outside of meander bends where the streamflow velocities are 

higher. Some of these sediments do not occur naturally and 

are associated with dikes that line the river. The D84 particle 

size of 0.33 mm in the meandering reach is medium sand and 

is not mobile at the lowest streamflow simulation. Sand in 

the meandering reach is more mobile at higher streamflows. 

Average and maximum grain shear stress increase more than 

an order of magnitude as streamflow increases from the lowest 

to the highest streamflow simulations (fig. 26), from 0.1 to 

1.3 N/m2 and 0.1 to 2.4 N/m2 for streamflow simulations 170 

and 2,270 m3/s. The contrast in sediment mobility between 

the meandering and straight reach shows that average and 

maximum grain shear stress for all five streamflow simulations 

is a factor of 2.5 and 2.7 greater in the straight reach compared 

to the meandering reach. 

Simulation of Flow and Sediment Mobility in the White Sturgeon Critical-Habitat Reach  47
Figure 26. Simulated sediment mobility and critical shear stress for five streamflows at cross sections positioned every 100 meters 

along the white sturgeon critical-habitat reach of the Kootenai River near Bonners Ferry, Idaho, and spawning event locations.

ID 91Z00_fig26

Average, 170 cubic meters per second (6,000 cubic feet per second)

Average, 566 cubic meters per second (20,000 cubic feet per second)

Average, 1,130 cubic meters per second (40,000 cubic feet per second)

Average, 1,700 cubic meters per second (60,000 cubic feet per second)

Average, 2,270 cubic meters per second (80,000 cubic feet per second)

Maximum, 170 cubic meters per second (6,000 cubic feet per second)

Maximum, 566 cubic meters per second (20,000 cubic feet per second)

Maximum, 1,130 cubic meters per second (40,000 cubic feet per second)

Maximum, 1,700 cubic meters per second (60,000 cubic feet per second)

Maximum, 2,270 cubic meters per second (80,000 cubic feet per second)

1 Approximate threshold of initiation of motion for medium gravel with a b-axis diameter of 8 to 16 mm on a level bed

2 Approximate threshold of initiation of motion for fine gravel with a b-axis diameter of 4 to 8 mm on a level bed

3 Approximate threshold of initiation of motion for very fine gravel with a b-axis diameter of 2 to 4 mm on a level bed

4 Approximate threshold of initiation of motion for coarse sand with a b-axis diameter of 0.5 to 1 mm on a level bed

5 Approximate threshold of initiation of motion for medium sand with a b-axis diameter of 0.25 to 0.5 mm on a level bed

0

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

2.2

2.4

2.6

2.8

3.0

3.2

3.4

3.6

3.8

4.0

4.2

4.4

4.6

4.8

5.0

5.2

5.4

5.6

5.8

6.0

6.2

6.4

6.6

6.8

7.0

7.2

7.4

7.6

7.8

8.0

8.2

8.4

8.6

8.8

9.0

SHIELDS CRITICAL SHEAR STRESS, IN NEWTONS PER SQUARE METER

0

1

2

3

4

5

6

7

8

9

228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246

DISTANCE ALONG MODEL REACH, IN RIVER KILOMETERS

GRAIN SHEAR STRESS IN NEWTONS PER SQUARE METER

3

4

2

5

1

Meander

Reach

Straight

Reach

STURGEON SPAWNING EVENTS PER UNIT OF EFFORT (SEPUE) DURING 1994-2001

20

40

SEPUE X

10,000

DEEP

CREEK

MYRTLE

SHORTY ISLAND CREEK

AMBUSH

ROCK

River Kilometers 229.6 - 231.45 River Kilometer 234.63 River Kilometer 240.25 River Kilometers 244.1 - 244.6

48  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Model Limitations

A fair evaluation of the applicability of the model 

to concerns about sturgeon spawning habitat requires 

consideration of potential modeling approach limitations, 

some of which are associated with the formulation of the 

model, and some of which are associated with limitations 

in the field data used to develop, calibrate, and validate the 

model. The model’s ability to simulate the velocity flow 

field, bed shear stress, and sediment mobility is constrained 

largely by (1) the accuracy and level of channel geometry 

detail, especially regarding errors that could arise because 

topography was measured during varying streamflows, 

because different streamflows were used in the model, and 

because the accuracy of the current topology available for 

Shorty Island is not known, (2) the way the relation between 

streamflow and bedforms was characterized, and (3) the 

potential errors incurred by applying a steady-state model 

to unsteady flow situations. Several minor potential sources 

of error also are in the model. For example, flow dynamics 

adjacent to anthropogenic or natural vertical obstructions 

in the flow field would be better described using a fully 

3-dimensional model. Similarly, the model treatment of 

turbulence is fairly simple because areas in the river with 

undulating and complex bathymetry most likely are areas 

where advection of turbulence and anisotropy in the turbulence 

field are important. Because of the complex computations, and 

the requirement to collect even more data, the beneficial return 

of an unsteady 3-dimensional, turbulence-resolving model 

probably is limited. 

Although the model was calibrated to a maximum 

streamflow of 2,540 m3/s, the calibration streamflows 

greater than 1,400 m3/s represent the pre-Libby Dam era, 

so the modern channel bathymetry used in the model may 

not accurately reflect the bed morphology present during 

those flows. On the basis of stream gaging measurements, 

Barton (2004) reported that the closure of Libby Dam did not 

influence the long-term mean elevation of the riverbed beneath 

the Copeland cableway: 524.7 m (n = 599) is the median 

value during the pre-Libby Dam era from 1929 through 1971 

and 524.7 m (n = 145) is the median value during the Libby 

Dam era from 1972 to 1993. The Copeland gaging station 

(12318500) is about 30.4 km below the downstream boundary 

of the model reach. Although strong evidence indicates that 

pre-dam and dam-era channel geometry generally are similar, 

the accuracy of streamflow simulations for pre-dam peak 

flows is expected be less than streamflow simulations for damera peak flows.

Velocity conditions at the upstream boundary of the 

model grid have a profound effect on the flow simulation 

for roughly the upper 1 km of the modeling reach. Velocity 

conditions have been specified at the upstream boundary 

in the model based on field measurements taken at the 

boundary during streamflows of 776 m3/s and 1,260 m3/s. 

Velocity boundary conditions likely will vary for streamflow 

conditions that are greater or less than streamflow during field 

measurements. 

Summary

In support of the Kootenai River White Sturgeon 

Recovery Team, the USGS developed, calibrated, and 

validated a multidimensional model for streamflow in the 

critical-habitat reach of the Kootenai River near Bonners 

Ferry, Idaho. The results of a few simple streamflow 

simulations and demonstrations of how the model can be used 

to link physical characteristics of streamflow to biological or 

other habitat data are presented, as well as model limitations. 

The model potentially is a useful tool for quantifying quality 

and quantity of white sturgeon spawning and rearing habitat, 

as well as for evaluating proposed habitat enhancement 

measures. 

During the field study, the channel geometry in the 

white sturgeon spawning reach was mapped with a horizontal 

accuracy of ±0.051 m and a vertical accuracy of ±0.041 m. 

In addition, the 1⁄2 phi particle-size distribution of riverbed 

sediments was determined, the degradation and aggradation 

of the Kootenai River channel were measured at five sites, and 

the amplitude and wavelength of dunes and other bedforms 

were monitored at five sites for streamflows of 229, 663, 

1,110, and 1,150 m3/s. The velocity structure of the river also 

was mapped in detail at 15 cross sections using an acoustic 

Doppler current profiler and mapping-grade global positioning 

system.

The USGS MultiDimensional Surface-Water Modeling 

System was used to construct a flow model for the criticalhabitat reach of the Kootenai River, between river kilometers 

(RKM) 228.4 and 245.9. The model reach is subdivided into 

two reaches based on the primary sediment forming the river 

substrate: (1) a straight reach with a sand, gravel, and cobble 

substrate between the upstream model boundary (RKM 

245.9) and the upstream end of Ambush Rock (RKM 244.6), 

and (2) a meandering reach consisting primarily of a sand 

substrate between the upstream end of Ambush Rock and the 

downstream model boundary. Near the downstream boundary, 

Shorty Island divides the flow into a main and a secondary 

channel. In addition, the model reach was divided into three 

velocity zones based on the velocity structure characteristics 

within each zone. The computational grid used to model 

Kootenai River was 17,525 m in length with 3,505 nodes in 

the downstream direction and 800 m in width with 161 nodes 

in the cross-stream direction, forming an approximately 

5.0- by 5.0-m grid.

The model was calibrated to 14 historical streamflow 

conditions ranging from 157 to 2,540 m3/s. Model calibration 

indicated that bedform-induced form drag is a significant 

fraction of the flow resistance in the Kootenai River for 

Summary  49
streamflow less than about 595 m3/s. Friction along the 

riverbed is increased at low streamflows due to formation 

of tall dunes, and friction decreases at higher streamflows 

because the dunes tend to wash out.

The model was validated by comparing simulated flow 

velocities with flow velocities measured at 15 cross sections 

between RKM 229.1 and 236.9 during steady streamflow 

that averaged 538 m3/s on August 12-14, 2003. The model 

simulates the magnitude and structure of flow across the 

section reasonably well, with a few notable exceptions. The 

model slightly under-simulated the magnitude and location 

of peak velocities in cross sections at the apex of bends in the 

river. This is a common result for models that are not fully 

3-dimensional, and can be attributed to the lack of secondary 

flow feedback on primary velocity distribution. Streamflow 

simulations for the first two sections in the main channel 

around Shorty Island (2313 and 2310) are notably poor. 

Validation of the model also included comparing measured 

and simulated vertical structure of downstream and crossstream velocities for the 15 cross sections. For downstream 

and cross-stream velocity, the streamflow simulations 

represent both the magnitudes and structure of flow reasonably 

well, including the position of the velocity maxima and the 

strength of the cross-stream flow.

The model’s ability to simulate the velocity flow field, 

bed shear stress, and sediment mobility is constrained largely 

by (1) the accuracy and level of channel geometry detail, 

especially regarding errors that could arise because topography 

was measured during varying streamflows and because 

different streamflows were used in the model, and because the 

accuracy of the current topology available for Shorty Island 

is not known, (2) the way the relation between streamflow 

and bedforms was characterized, and (3) the potential errors 

incurred by applying a steady-state model to unsteady flow 

situations. Although strong evidence indicates that pre-dam 

and dam-era channel geometry generally are similar, the 

accuracy of streamflow simulations for pre-dam peak flows 

is expected be less than streamflow simulations for dam-era 

peak flows. Velocity conditions at the upstream boundary of 

the model grid have a profound effect on the flow simulation 

for roughly the upper 1 km of the modeling reach. Velocity 

conditions have been specified at the upstream boundary in 

the model based on field measurements taken at the boundary 

during streamflows of 776 m3/s and 1,260 m3/s. Velocity 

boundary conditions may vary for streamflow conditions that 

are greater or less than streamflow during field measurements. 

The MultiDimensional Surface-Water Modeling System

model was used to simulate the water-surface elevation, depth, 

velocity flow field, bed shear stress, and sediment mobility 

for the study reach in the Kootenai River for the same range 

of streamflows used in calibration. Spawning events per unit 

of effort during 1994-2001 in the white sturgeon criticalhabitat reach are graphically presented along with modeling 

results. A few simple simulations demonstrate how the model 

can be used to link physical characteristics of streamflow 

to biological or other habitat data. Some measures of depth, 

velocity, and substrate composition generally are considered 

when assessing sturgeon spawning habitat. Habitat suitability 

curves developed for white sturgeon in the Lower Columbia 

River were used to characterize conditions in the Kootenai 

River spawning habitat. Requirements for Kootenai River 

white sturgeon spawning habitat may vary from that in the 

Lower Columbia River; however, both rivers are highly 

regulated. 

The modeling results do not support the hypothesis that 

the relative location of free-flowing and backwater streamflow 

may play a role in influencing white sturgeon spawning 

patterns. During 2001, spawning occurred further upstream 

than any other time during 1994-2001, at the same time, freeflowing streamflow was further downstream than any other 

spawning event during the same period. The 2001 observations 

appear not to support the hypothesis that the upstream extent 

of sturgeon spawning is set by the location of the backwater 

transition. 

Egg collection on the Kootenai River during the past 

12 spawning seasons shows that sturgeon eggs tend to 

accumulate in the thalweg, where depths can exceed 14 m. 

Habitat suitability in the straight reach ranges from poor to 

excellent and in the meandering reach is generally excellent. 

Although a comparison of simulated river depth and sturgeon 

spawning event locations (egg locations) in the critical-habitat 

reach indicate that egg locations are preferentially found in 

deeper areas, careful analysis suggests that this is only a weak 

positive correlation. Eggs are only slightly more likely to be 

found in deeper parts of the river. This correlation becomes 

slightly stronger if simulation results upstream of Ambush 

Rock (in the straight reach) are neglected. 

Studies on the Columbia River indicate that sturgeon 

seek areas of high velocity for spawning. In other studies, lake 

sturgeon were found to spawn in tributary rapids. Spawning 

habitat suitability for streamflow velocity in the model was 

evaluated. In the meander reach, the average velocity at 

streamflows of 1,700 and 2,270 m3/s is classified moderate 

except for parts of the reach at Shorty Island, where velocity 

is classified poor; streamflows of 1,130 m3/s and less are 

classified poor. In the straight reach, the average velocity 

at all streamflows is classified poor to moderate except at a 

streamflow of 170 m3/s, which is classified poor throughout 

the reach. 

Streamflow velocities equal to or greater than 1.0 m/s 

are believed to greatly reduce or eliminate predation of 

white sturgeon eggs. The simulated average velocity in the 

main channel at Shorty Island, where white sturgeon most 

frequently spawn, does not approach 1.0 m/s until streamflow 

is 2,270 m3/s, and this only occurs near RKM 231.1. However, 

maximum simulated velocity in the spawning reach is greater 

than 1.0 m/s for flows equal to and greater than a streamflow of 

1,130 m3/s. 

50 Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Quantification of sediment mobility provides preliminary 

insight into streamflow requirements for flushing silt and 

sand currently burying gravel and cobble substrate that could 

be used for spawning and egg incubation. Very-fine to fine 

gravel is mobile in the straight reach for all five streamflow 

simulations; however, at the lowest streamflow of 170 m3/s 

gravel is mobile in only the upper half of the reach. Very 

coarse sand is not mobile for about the lower third of the 

straight reach for the 170 m3/s streamflow simulation. Gravel 

becomes slightly more mobile at higher streamflows. In 

contrast to the straight reach, very fine gravel (b-axis diameter 

of 2.0 mm) is mobile in the meandering reach for only the 

three highest streamflow simulations of 1,130, 1,700, and 

2,270 m3/s.

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Columbia River Power System: Portland, Oregon, variously 

paginated.

52  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Appendix A. Processing Acoustic 

Doppler Current Profiler Data

Spatial Mapping of Bed Elevation

The acoustic Doppler current profile (ADCP) measures a 

separate distance to the riverbed along each of four transducer 

beams. The four bed elevations at the point of beam contacts 

were computed using a custom algorithm (Dinehart and 

Burau, 2005). Points of bed elevation, accumulated over 

ADCP survey paths, were sufficient and widespread enough to 

allow useful extraction of a bathymetric surface. Each crossing 

path was offset from a previous path, which generated a 

distribution of bed-elevation points through the cross section. 

A bathymetric surface was created by interpolation of 1,000 

points or more to a rectangular grid enclosing the range of 

crossing paths.

Velocity Ensembles

The ADCP velocity ensembles were filtered and 

smoothed by a series of algorithm passes (Dinehart and Burau, 

2005). One pass removed statistical outliers of velocityvector components at the bottom of each ensemble. Another 

pass numerically smoothed velocity data in two steps. Vector 

components exceeding the ensemble mean by 2.5σ (standard 

deviation) were first replaced directly by an average of nearest 

neighbors, removing extreme outliers that originate with 

velocity ambiguity of the ADCP. This operation was followed 

by a centered, three-point average applied to all interior 

components of velocity ensembles, using the formula,

(1)

where ub signifies a vector component u, v, or w at an interior 

bin, and b ranges from N=2 to N= (number of bins -1).

The irregular paths followed in ADCP surveys produced 

a curvilinear mesh of velocity ensembles when plotted in the 

channel reach. The sampled velocity ensembles were realigned 

and interpolated to regular grids for averaging different 

ensembles at similar positions. Previous studies of ADCP 

surveys have shown that secondary flows can be resolved by 

averaging multiple crossings of bends (Dinehart and Burau, 

2005). 

To derive a linear grid of averaged ADCP velocity 

vectors, it was necessary to translate the irregular positions 

of velocity ensembles in survey paths to the same linear cross 

section. Therefore, a procedure of “section straightening” 

was used to translate velocity ensembles spatially to a straight 

line. A mean crossing line was fit through a set of crossing 

paths to ensure that ensembles were translated minimally 

over measured bathymetry. The position of each ensemble 

was translated to the crossing line. The distance L from a 

distant start point of the crossing line (xs, ys) to each ensemble 

location (xe, ye) was calculated and applied with the angle θ of 

the crossing line above the x-axis in the form,

 ,

(2)

to yield translated points xt and yt for each ensemble. Although 

some velocity ensembles were translated by several meters, 

the distance of translation was usually less than 10 percent of 

the channel width.

Grid Interpolation and Averaging

Flow-field ADCP data collected by repeated crossings 

were interpolated to 2-dimensional cross-sectional grids. 

The grids were constructed to match the bathymetric surface 

and water-surface elevations of the surveyed cross sections. 

A rectangular grid with specified i-j dimensions was created 

and then modified to match the cross-sectional bathymetry 

and vertical-spacing requirements. Lateral nodes across 

the channel were ordered by the i increment. Distances 

between i nodes approximated the original spacing of velocity 

ensembles. This usually yielded cell widths of 0.5 to1 meter 

(m). Vertical j nodes at each i increment were extended to the 

bed from the water-surface elevation. Cell heights were set 

to approximate the original bin height (0.25 m) used during 

ADCP surveys. 

The number of j nodes in a grid was calculated from the 

maximum depth in the cross section and the cell height. To 

maintain constant cell heights over irregular bathymetry in 

an ordered grid, extra j nodes were assigned closely spaced 

elevations within 0.3 m of the lower bathymetric boundary. 

This configuration was chosen to (1) maintain uniform vertical 

spacing of vector components over the measured range of 

velocity, and (2) isolate the extra j nodes within the near-bed 

region that was unmeasurable by ADCPs. By interpolating 

ADCP crossings to 2-dimensional cross-sectional grids, 

the random sequence of distances between ensembles was 

u u u u b b b b = + + − + 0 24 0 5 0 25 1 1 . . . , 

x x L

y y L

s

s

1

1

= +

= +

cos( )

sin( )

θ

θ

Appendix A. Processing Acoustic Doppler Current Profiler Data  53
replaced by regular intervals of velocity profiles. The velocity 

vectors were interpolated in Tecplot by an inverse-distance 

algorithm of the form

(3)

where φd and φs are the variable values at the grid nodes and in 

the ensembles, respectively. The weighting function, ws, was 

set equal to 1/D3.5, where D is the distance between the random 

ensemble point and the target grid point. The algorithm 

weights a number of nearby vectors (source vectors) to derive 

a new vector value at each interpolated-grid node (target 

node). Each vector at a target node was interpolated from six 

source vectors chosen by an equipartite arrangement around 

the target node. This arrangement prevented the algorithm 

from selecting source vectors on only one side of the target 

node, or only source vectors within the same ensemble. With 

the high spatial density of source vectors and the low number 

used for interpolation, target vectors represented only the 

nearest ensembles of the source mesh.

To average multiple ADCP surveys, multiple grids 

of identical dimensions were created. Velocity vectors 

in each ADCP survey were interpolated to a single grid 

by weighting several source vectors to each target node. 

Vectors from all interpolated grids were then averaged at 

corresponding grid nodes. The ensembles of any ADCP 

survey are spaced variably because boat speed varies. If the 

set of ADCP surveys was averaged directly to a single grid, 

slow crossings would be weighted more than rapid crossings. 

φ φ

d s s

s

w

w = ∑

∑ ,

Therefore, an interpolation step was required first to yield a 

time-averaged velocity field with statistical validity. Inversedistance interpolation of ADCP data provided only a first 

approximation of mean velocity fields because turbulent 

structures across velocity ensembles remained in the processed 

ADCP surveys.

From the central limit theorem, the standard deviation 

of many averaged crossings is expected to approach the 

population standard deviation. Averaging of N crossings at 

straight reaches showed that standard deviations of crossstream and vertical velocities were proportional to 1/N-0.5, 

and trended toward zero at large N. For vector components 

with a near-zero mean over time (cross-stream and vertical 

velocities), averages of multiple crossings approached their 

means rapidly with about six crossings (Randall Dinehart, U.S. 

Geological Survey, written commun., 2004), using the ADCP 

settings specified earlier. Standard deviations of streamwise 

components were less reduced because they reflected vertical 

and lateral variations in velocity profiles across the channel.

After averaged grids were prepared from multiple ADCP 

surveys, the vector components at each i node were averaged 

over the vertical.

References

Dinehart, R.L., and Burau, J.R., in press, Repeated surveys 

by acoustic Doppler current profiler for flow and sediment 

dynamics in a tidal river: Journal of Hydrology.

54  Simulation of Flow and Sediment Mobility Using Multidimensional Model, Kootenai River near Bonners Ferry, Idaho
Manuscript approved for publication, October 20, 2005

Prepared by the U.S. Geological Survey Publishing staff 

Tacoma Publishing Service Center

Bill Gibbs 

Debra Grillo

Ginger Renslow

Bobbie Jo Richey

Judy Wayenberg

For more information concerning the research in this report, contact the

Director, Idaho Water Science Center 

230 Collins Road

Boise, ID 83702

http://id.water.usgs.gov
SIR 2005–5230 Barton and others Simulation of Flow and Sediment Mobility Using a Multidimensional Flow Model for the White Sturgeon Critical-Habitat Reach, Kootenai River near Bonners Ferry, Idaho