Prepared in cooperation with the 

Kootenai Tribe of Idaho

Characterization of Channel Substrate and 

Changes in Suspended-Sediment Transport 

and Channel Geometry in White Sturgeon 

Spawning Habitat in the Kootenai River near 

Bonners Ferry, Idaho, Following the Closure 

of Libby Dam

Water-Resources Investigations Report 03–4324

Version 1.0

U.S. Department of the Interior

U.S. Geological Survey

Click here for colored version of cover

USGS

science for a changing world
Characterization of Channel Substrate, and 

Changes in Suspended-Sediment Transport and 

Channel Geometry in White Sturgeon Spawning 

Habitat in the Kootenai River near Bonners Ferry, 

Idaho, Following the Closure of Libby Dam

Prepared in cooperation with the

KOOTENAI TRIBE OF IDAHO

Water-Resources Investigations Report 03-4324

Version 1.0

By Gary J. Barton

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia; 2004

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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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.

Barton, G.J., 2004, Characterization of Channel Substrate, and Changes in Suspended-Sediment Transport and 

Channel Geometry in White Sturgeon Spawning Habitat in the Kootenai River near Bonners Ferry, Idaho, Following the 

Closure of Libby Dam: Water-Resources Investigations Report 03–4324, 102 p.
Contents iii

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

Introduction ...................................................................................................................................................... 3

Purpose and Scope .................................................................................................................................. 3

Acknowledgments................................................................................................................................... 4

Description of Study Area................................................................................................................................ 4

Kootenai River Watershed....................................................................................................................... 4

Geology of the Kootenai River Basin ..................................................................................................... 6

Geomorphology of the Kootenai River Below Libby Dam .................................................................... 7

Study Methods.................................................................................................................................................. 7

Measuring Streamflow and the Concentration of Suspended Sediment................................................. 7

River Channel Geometry Computation................................................................................................... 8

Mapping of Channel Substrate................................................................................................................ 8

Seismic-Subbottom Profiling......................................................................................................... 8

Coring of Riverbed Sediment ........................................................................................................ 10

Limitations on Mapping Channel Substrate .................................................................................. 10

Changes in Streamflow and Suspended-Sediment Regimes............................................................................ 10

Streamflow .............................................................................................................................................. 11

Suspended-Sediment Regime.................................................................................................................. 13

Hysteresis Effect on Transport of Suspended Sediment ......................................................................... 14

Suspended-Sediment Transport During the 1974 White Sturgeon Recruitment .................................... 14

Suspended-Sediment Particle Size.......................................................................................................... 16

Changes in Channel Geometry and Substrate.................................................................................................. 16

Channel Geometry .................................................................................................................................. 16

Channel Width and Migration........................................................................................................ 17

Aggradation and Degradation of Riverbed .................................................................................... 17

Composition of Channel Substrate ......................................................................................................... 17

General Description of Substrate................................................................................................... 18

Braided Reach................................................................................................................................ 18

Buried Gravel-Cobble Reach......................................................................................................... 19

Meander Reach .............................................................................................................................. 19

Upstream from Myrtle Creek................................................................................................ 19

Downstream from Myrtle Creek........................................................................................... 20

Shorty Island......................................................................................................................... 20

Effects of Changes in Suspended-Sediment Transport and Channel Substrate on White 

Sturgeon Spawning Substrate ................................................................................................................. 21

Summary and Conclusions............................................................................................................................... 22

References Cited .............................................................................................................................................. 23

CONTENTS
iv Suspended-Sediment Transport, Kootenai River, Idaho

Figures

Figure 1. Map showing location of the 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. .................................................................................................... 2

Figure 2. Maps showing locations of cross sections, seismic subbottom profiles, riverbed sedimentcore samples, and white sturgeon spawning reaches in the study area on the Kootenai River 

near Bonners Ferry, Idaho [3 pages]. ........................................................................................... 25

Figure 3. Graph showing generalized stage of the Kootenai River along three types of geomorphologic 

reaches from below the mouth of the Moyie River to Copeland, Idaho....................................... 5

Figure 4. Graph showing monthly median water levels on Kootenay Lake at Proctor (1924–30) 

and Queens Bay (1931–2000), British Columbia, Canada .......................................................... 6

Figure 5. Map showing geomorphologic reaches and selected streamflow-gaging stations on 

the Kootenai River between Crossport, Idaho, and Kootenay Lake, British Columbia, Canada. 28

Figure 6. Seismic subbottom profile showing sand dunes on the riverbed near the center of the

Kootenai River approximately 1.1 to 1.2 kilometers upstream from Shorty Island, June 1999 .. 29

Figure 7. Photograph showing seismic subbottom profiling system ........................................................... 30

Figure 8. Photograph showing U.S. Geological Survey personnel collecting a 3.7-meter-long 

vibracore sample of riverbed sediments in the Kootenai River, Idaho ......................................... 31

Figure 9. Graphs showing annual streamflow and suspended-sediment load, 1966–83, and annual 

median daily streamflow and suspended-sediment load for the pre-Libby Dam era (1966–71) 

and Libby Dam era (1973–83) in the Kootenai River at Copeland, Idaho................................... 32

Figure 10. Graph showing streamflow at U.S. Geological Survey streamflow-gaging station 12322000

on the Kootenai River at Porthill, Idaho, 1929–2000 ................................................................... 12

Figure 11. Graph showing relation between stream discharge and streamflow velocity at U.S. Geological 

Survey streamflow-gaging station 12318500 on the Kootenai River at Copeland, 

Idaho, 1929–93. ............................................................................................................................ 12

Figure 12. Graph showing suspended-sediment transport on the Kootenai River at Copeland, Idaho, 

and near Libby, Montana, 1966–2000.......................................................................................... 33

Figure 13. Graph showing comparison of the duration for daily mean flows during the pre-Libby Dam 

era and Libby Dam era at U.S. Geological Survey streamflow-gaging station 12322000 on 

the Kootenai River at Porthill, Idaho, 1929–2000 ....................................................................... 13

Figure 14. Graphs showing daily suspended-sediment concentration and mean daily streamflow at U.S. 

Geological Survey streamflow-gaging station 12318500 on the Kootenai River at Copeland, 

Idaho during the pre-Libby Dam and Libby Dam eras [2 pages]................................................ 34

Figure 15. Graph showing distribution of particle size in suspended-sediment samples collected at U.S. 

Geological Survey streamflow-gaging station 12318500 on the Kootenai River at Copeland, 

Idaho, 1968–76 ............................................................................................................................. 15

Figure 16. Graph showing changes in channel geometry on the Kootenai River beneath the stationary 

cableway at U.S. Geological Survey streamflow-gaging station 12318500 at Copeland, 

Idaho, 1931–93 ............................................................................................................................. 36

Figure 17. Graph showing fluctuation of minimum riverbed elevation with streamflow for the pre-Libby 

Dam and Libby Dam eras on the Kootenai River beneath the stationary cableway at U.S. 

Geological Survey streamflow-gaging station 12318500 at Copeland, Idaho, 1929–93.............. 16

Figure 18. Graphs showing streamflow, mean riverbed elevation, and thalweg elevation on the Kootenai 

River beneath the stationary cableway at U.S. Geological Survey streamflow-gaging station 

12318500 at Copeland, Idaho, 1929–93 ....................................................................................... 37
Figure 19. Diagrams showing composition of sediment cores penetrating riverbed deposits in the white 

sturgeon spawning reaches of the Kootenai River near Bonners Ferry, Idaho [5 pages] ............. 38

Figure 20. Photograph showing alluvial sand with lamina of organic debris in middle section of 

riverbed sediment core K11-LB taken near the left bank of the Kootenai River at river 

kilometer 235.1 ............................................................................................................................. 43

Figure 21. Maps showing geologic composition of the channel substrate between river kilometers 246.7 

and 225 of the Kootenai River near Bonners Ferry, Idaho [3 pages]............................................ 44

Figure 22. Photograph showing alluvial sand layer overlying a layer of gravel, cobble, sand, and organic 

debris that are unconformably deposited on lacustrine clay in a sediment core sample taken 

near the right bank of the Kootenai River at river kilometer 241.7.............................................. 43

Figure 23. Seismic subbottom profiles showing geologic composition of the channel substrate at

cross-sections A-A' through S-S' on the Kootenai River near Bonners Ferry, Idaho [19 pages] See Below

Explanation for Figures 24A through 24II....................................................................................................... 66

Figure 24. Geologist striplog of sediment cores taken in the channel substrate of the Kootenai 

River near Bonners Ferry, Idaho [35 pages]............................................................................... See Below

Figures 23 and 24 are multipage figures. Click on each figure to view them individually.

Figure 23A

Figure 23B

Figure 23C

Figure 23D

Figure 23E

Figure 23F

Figure 23G

Figure 23H

Figure 23I

Figure 23J

Figure 23K

Figure 23L

Figure 23M

Figure 23N

Figure 23O

Figure 23P

Figure 23Q

Figure 23R

Figure 23S

Tables

1. Sediment cores of the Kootenai River bed near Bonners Ferry, Idaho, October 19–22, 2000................... 9

2. Sediment samples of Kootenai River bed taken with ponar dredge sampler on June 20, 2000 ................. 11

Figure 24A

Figure 24B

Figure 24C

Figure 24D

Figure 24E

Figure 24F

Figure 24G

Figure 24H

Figure 24I

Figure 24J

Figure 24K

Figure 24L

Figure 24M

Figure 24N

Figure 24O

Figure 24P

Figure 24Q

Figure 24R

Figure 24S

Figure 24T

Figure 24U

Figure 24V

Figure 24W

Figure 24X

Figure 24Y

Figure 24Z

Figure 24AA

Figure 24BB

Figure 24CC

Figure 24DD

Figure 24EE

Figure 24FF

Figure 24GG

Figure 24HH

Figure 24II

Contents v
CONVERSION FACTORS 

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

kilometer (km) 0.6214 mile (mi)

meter (m) 3.281 foot (ft)

millimeter (mm) 0.03937 inch (in.)

Area

square kilometer (km2) 247.1 acre

square kilometer (km2) 0.3861 square mile (mi2)

Volume

cubic meter per day (m3/d) 35.31 cubic foot per day (ft3/d)

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

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

cubic meter per second (m3/s) 35.31 cubic foot per second (ft3/s)

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

Mass

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

Temperature in degrees Celsius (oC) may be converted to degrees Fahrenheit (oF) as follows:

oF=1.8 oC+32.

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

micrograms per liter (mg/L).

Sea level: In this report, “sea level” refers to the National Geodetic Vertical Datum of 1929 (NGVD 

of 1929)—a geodetic datum derived from a general adjustment of the first-order level nets of both the 

United States and Canada, formerly called Sea Level Datum of 1929. 

vi Suspended-Sediment Transport, Kootenai River, Idaho
Abstract

Many local, State, and Federal agencies have concerns over the declining population of white sturgeon 

(Acipenser transmontanus) in the Kootenai River and the 

possible effects of the closure and subsequent operation of 

Libby Dam in 1972. In 1994, the Kootenai River white 

sturgeon was listed as an Endangered Species. A year-long 

field study was conducted in cooperation with the Kootenai 

Tribe of Idaho along a 21.7-kilometer reach of the Kootenai 

River including the white sturgeon spawning reach near 

Bonners Ferry, Idaho, approximately 111 to 129 kilometers 

below Libby Dam. During the field study, data were 

collected in order to map the channel substrate in the white 

sturgeon spawning reach. These data include seismic subbottom profiles at 18 cross sections of the river and sediment cores taken at or near the seismic cross sections. The 

effect that Libby Dam has on the Kootenai River white 

sturgeon spawning substrate was analyzed in terms of 

changes in suspended-sediment transport, aggradation and 

degradation of channel bed, and changes in the particle size 

of bed material with depth below the riverbed.

The annual suspended-sediment load leaving the 

Kootenai River white sturgeon spawning reach decreased 

dramatically after the closure of Libby Dam in 1972: mean 

annual pre-Libby Dam load during 1966–71 was 1,743,900 

metric tons, and the dam-era load during 1973–83 was 

287,500 metric tons. The amount of sand-size particles in 

three suspended-sediment samples collected at Copeland, 

Idaho, 159 kilometers below Libby Dam, during spring and 

early summer high flows after the closure of Libby Dam is 

less than in four samples collected during the pre-Libby 

Dam era. The supply of sand to the spawning reach is 

currently less due to the reduction of high flows and a loss 

of 70 percent of the basin after the closure of Libby Dam. 

The river’s reduced capacity to transport sand out of the 

spawning reach is compensated to an unknown extent by a 

reduced load of sand entering the spawning reach.

Since the closure of Libby Dam, the most notable 

change in channel geometry at the Copeland streamflowgaging station was the initiation of cyclical aggradation and 

degradation of the riverbed in the center of the channel. The 

aggradation and degradation of the riverbed are reflected in 

a twofold increase, from 1.3 to 2.5 meters, in the fluctuation 

of the minimum riverbed elevation, which suggests that 

during the Libby Dam era, parts of the riverbed in the 

spawning reach may have aggraded or degraded by as much 

as 2.5 meters.

Before the closure of Libby Dam, there was a greater 

propensity for aggradation and degradation of sand over the 

discontinuous gravel and cobble layers in the buried gravelcobble reach at Bonners Ferry. The gravel and cobble in this 

reach, 111.3 to 115.9 kilometers below Libby Dam, are 

buried by sand. Unregulated spring snowmelt-runoff flows 

flushed part of the sand layer and exposed some of the 

buried gravel-cobble layer because streamflow velocities 

were higher at that time. Unregulated autumn-winter base 

flows gradually deposited silt and sand and reestablished a 

sand layer, burying the gravel-cobble layer. This cyclical 

process of aggradation and degradation of the riverbed sediment is reflected in the alternating gravel-cobble layers and 

sand layers found in sediment core K18-TH taken as part of 

this project.

White sturgeon spawning substrate in the Kootenai 

River meander reach is currently composed of alluvial sand 

that forms sand dunes and of minor amounts of lacustrine 

clay and silt that generally are found in the river’s thalweg. 

The present substrate composition in the meander reach is 

considered similar to that which existed prior to closure of 

Libby Dam, with one possible exception. Prior to closure of 

Libby Dam, minor amounts of gravel and cobble may have 

been exposed on the riverbed in the spawning reach just 

below the mouth of Myrtle Creek 230 kilometers below 

Libby Dam. The substrate composition near Shorty Island, 

234 kilometers below Libby Dam, a notable white sturgeon 

Characterization of Channel Substrate, and Changes in 

Suspended-Sediment Transport and Channel Geometry 

in White Sturgeon Spawning Habitat in the Kootenai 

River near Bonners Ferry, Idaho, Following the Closure 

of Libby Dam

By Gary J. Barton
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12318500

12304500

12301933 12302055

0

0 20 40 60 80 KILOMETERS

20 40 MILES

Base from U.S. Geological Survey

digital data, 1:100,000, 1980

Albers Equal-Area projection

Standard parallels 43 30', 47 30',

and -114 00', 41 45'

No false easting or false northing

115¡ 115 00' ¡ 115 20' ¡ 116 40' ¡ 00' 116¡ 20' 116¡ 40' 117¡ 00' 117¡ 117 20' ¡ 40'

118¡ 00'

48¡ 20'

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EXPLANATION

Expanded area shown in figure 5

U.S. Geological Survey gaging

 station and identifier

West Kootenay Power and Light

 gaging station

12318500

CANADA

UNITED STATES

Kootenai River

Drainage Basin

Figure 1. Location of the 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.

2 Suspended-Sediment Transport, Kootenai River, Idaho
spawning reach, is predominantly sand and is similar to that 

which existed prior to closure of Libby Dam. 

INTRODUCTION

Many local, State, and Federal agencies have concerns about the declining population of white sturgeon 

(Acipenser transmontanus) in the Kootenai River in Idaho. 

In 1994, the Kootenai River white sturgeon was listed as an 

Endangered Species, and fishing was prohibited. The white 

sturgeon population decline is reflected in fewer juvenile 

sturgeon and an overall decline in spawning success. The 

last successful recruitment of white sturgeon occurred in 

1974 (U.S. Fish and Wildlife Service, 1999). Recruitment 

occurs when a spawning event produces juvenile fish that 

survive to create a new year-class of fish in sufficient numbers to maintain the fish population. Lack of recruitment has 

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

streamflow regime of the Kootenai River after closure 

(completion) of Libby Dam, near Libby, Montana, in 1973 

because these changes could have altered the channel substrate and sturgeon spawning habitat near Bonners Ferry, 

Idaho (fig. 1; Collier and others, 1996). Other changes in the 

Kootenai River that could have affected the spawning substrate are the construction of dikes on the natural levees, 

changes in backwater conditions near Bonners Ferry caused 

by changes in the level of Kootenay Lake, and loss of 

wetlands in the river valley.

White sturgeon are broadcast spawners that release 

adhesive, negatively buoyant eggs that sink to the riverbed 

(Stockley, 1981; Brannon and others, 1984). Paragamian 

and others (2001; 2002) identified five primary reaches in 

the Kootenai River downstream from Bonners Ferry where 

white sturgeon spawned during 1994–99. These investigators collected most sturgeon eggs in the outsides of 

riverbends in the thalweg (the deepest part of any cross 

section of a river). Parsley and others (1993, p. 224) reported that in the Lower Columbia River, most sturgeon 

eggs were collected over substrates of cobble or boulder, 

where the eggs are sheltered by attaching to and incubating 

on the rocky substrate. Rocky substrate also provides cover 

for yolk sac larvae before they become free swimming.

Egg suffocation and predation have been hypothesized as potential factors for white sturgeon egg mortality in 

the Kootenai River (Anders and Richards, 1996; Paragamian and Kruse, 1996; and U.S. Fish and Wildlife Service, 

1999). More than 96 percent (428 of 444) of the naturally 

produced white sturgeon eggs collected between 1991 and 

1995 in this reach were from sand substrate that appeared to 

be suboptimal for incubation (Anders and Richards, 1996; 

Paragamian and Kruse, 1996). The hypothesis of egg suffocation is supported by the observation that mats placed on 

the riverbed to catch sturgeon eggs typically are buried by 

sand within 48 hours of deployment (Vaughn Paragamian, 

Idaho Department of Fish and Game, and Sue Ireland, 

Kootenai Tribe of Idaho, oral commun., 1999). Gravel and 

cobble are optimal substrate for sturgeon spawning habitat, 

whereas sand is considered detrimental.

In 2000–2001, the U.S. Geological Survey (USGS), 

in cooperation with the Kootenai Tribe of Idaho (KTOI), 

conducted a study to assess changes in suspended-sediment 

transport and channel substrate in the Kootenai River near 

Bonners Ferry, between RKM (river kilometers) 225 and 

246.7, after closure of Libby Dam in 1972, and the effects 

of any changes on the substrate in the white sturgeon 

spawning reaches there. Historical data on streamflow and 

suspended sediment in the Kootenai River and tributaries 

were used to determine suspended-sediment transport 

during the pre-Libby Dam and Libby Dam eras, and sediment cores and seismic subbottom profiles of the Kootenai 

River bed in the study area were analyzed to describe 

channel substrate during each era.

The Kootenai River White Sturgeon Recovery Team, 

composed of scientists and engineers from several local, 

State, Federal, and Canadian agencies, is trying to reestablish the recruitment of white sturgeon. Recognizing this, the 

USGS is conducting several studies that will provide the 

recovery team with information and tools that may help to 

reestablish recruitment. These tools will, among other objectives, allow investigators to assess the potential for enhancing the quality of the white sturgeon spawning substrate. 

Purpose and Scope

This study is part of an overall effort by local, State, 

and Federal agencies and the Kootenai Tribe of Idaho to 

improve the Kootenai River white sturgeon spawning habitat. The purposes of this report are to (1) describe the physical characteristics of the channel substrate in the Kootenai 

River between RKM 225 and 246.7—132 to 110.3 RKM 

below Libby Dam—before and after closure of Libby Dam, 

(2) assess the changes in suspended-sediment transport resulting from changes in streamflow after closure of the dam, 

and (3) assess the possible effects of these changes on the 

substrate in the white sturgeon spawning reaches of the 

study area. The report documents changes in (1) suspendedsediment transport, (2) channel geometry, and (3) sediment 

texture of channel substrate before and after dam closure. 

The scope of the study included (1) analyzing historical data 

on streamflow and suspended-sediment loads in the Kootenai River and tributaries, water levels in Kootenay Lake, 

particle-size distribution of suspended sediment, and channel geometry of the Kootenai River at Copeland, Idaho; and 

(2) collecting sediment cores and seismic subbottom profiles 

of the Kootenai River bed in the study area. The study inIntroduction 3
cluded data from streamflow-gaging stations (hereafter 

referred to as gaging stations or gages) in Idaho, Montana, 

and British Columbia. Because there were no gaging 

stations located in the study reach, the gaging station at 

Copeland, the closest to the study reach, was used as a 

surrogate to assess changes in channel geometry.

Acknowledgments

I would like to thank the people of the Kootenai River 

valley for their support of this project. I also appreciate Sue 

Ireland of the Kootenai Tribe of Idaho for providing the 

U.S. Geological Survey with boats for seismic surveys and 

for river-sediment coring operations. Vaughn Paragamian of 

the Idaho Department of Fish and Game provided information about the location of white sturgeon spawning 

reaches. Peter Van Metre, Michael Dorsey, Barbara Mahler, 

Keith Ludwig, and Marcus Gary, U.S. Geological Survey 

scientists from offices in Texas and Florida, conducted the 

river-sediment coring operations. Eric White of the U.S. 

Geological Survey in Connecticut assisted with the river 

seismic survey. Sabrina Conti, U.S. Geological Survey 

scientist in Idaho, transcribed archived stream-geometry 

data into spreadsheets and assisted with graphical analysis 

of the data. Kim Trask, student with the U.S. Geological 

Survey in Washington, assisted with graphical analysis and 

prepared geologic striplogs.

DESCRIPTION OF STUDY AREA

The Kootenai River begins in British Columbia, 

Canada, and flows through Montana and Idaho (fig. 1). 

Libby Dam is located on the Kootenai River 16 RKM 

upstream from Libby, Montana. The study area is the reach 

of the Kootenai River near Bonners Ferry, Idaho, from 

RKM 246.7 to 225 (approximately 111 to 129 RKM below 

Libby Dam), which includes the spawning habitat for the 

Kootenai River population of white sturgeon (fig. 2). Five 

reaches in the study reach were used by sturgeon for 

spawning between 1994 and 1999 (in descending order of 

number of eggs collected from the riverbed): Middle Shorty 

Island, RKM 230.0 to 231.0; upstream from Myrtle Creek, 

RKM 236.1 to 236.9; downstream from Deep Creek, RKM 

238.9 to 239.9; downstream from Myrtle Creek, RKM 233.5 

to 234.7; and below Shorty Island, RKM 228.0 to 229.0 

(Paragamian and others, 2001; 2002). Sturgeon were 

detected spawning as far upstream as Bonners Ferry only 

during the 2001 season, near RKM 245.6 (Vaughn 

Paragamian, Idaho Department of Fish and Game, oral 

commun., 2001). 

Kootenai River Watershed

The Kootenai River Basin is an international 

watershed that drains parts of British Columbia, Montana, 

and Idaho (fig. 1). (“Kootenai” is spelled “Kootenay” in 

Canada.) The Kootenai River drainage basin is located 

within the Northern Rocky Mountains physiographic 

province, which is characterized by north- to northwesttrending mountain ranges. The Continental Divide forms 

much of the eastern basin boundary, the Selkirk Mountains 

form the western basin boundary, and the Cabinet 

Mountains form the southern basin boundary. The Kootenai 

River is 721 km long and drains an area of 45,584 km2

. The 

river’s elevation is 3,618 m at its headwaters in British 

Columbia. Kootenai Falls, a 61-m-high waterfall and natural 

fish-migration barrier, is located 46 RKM downstream from 

Libby Dam. At Bonners Ferry, located 111 RKM below 

Libby Dam, near the upstream end of the white sturgeon 

habitat, the 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 flows toward the northwest in a 

meandering course through the broad, flat bottomlands referred to as Kootenai Flats (fig. 2) for about 80 km to the 

head of Kootenay Lake in British Columbia located 235 

RKM below Libby Dam. The Kootenai River flows from 

the West Arm of Kootenay Lake for about 32 km and 

empties into the Columbia River at Castlegar, British 

Columbia. 

A natural barrier at Bonnington Falls, now a series of 

four dams including the Corra Lynn Dam, isolates fish from 

other populations in the Columbia River Basin. The natural 

barrier has isolated sturgeon for approximately 10,000 years 

(Northcote, 1973). 

The river’s elevation is about 532 m at the confluence 

with Kootenay Lake. The main body of Kootenay Lake 

occupies 104 km of the length of the Purcell Trench. Water 

in Kootenay Lake backs up into the Kootenai River. Backwater conditions in the Kootenai River constantly prevail 

below the mouth of Deep Creek (116.7 RKM below Libby 

Dam) near Bonners Ferry, and during May, June, and July, 

can extend a few kilometers upstream from the U.S. 95 

Bridge (111 RKM below Libby Dam) at Bonners Ferry 

(fig. 3). During periods of low flow, free-flowing water may 

extend a few kilometers downstream from the U.S. 95 

Bridge.

The Kootenai watershed has undergone many changes 

due to loss of wetlands, construction of dikes on the natural 

levees, changes in backwater conditions because of changes 

in the level of Kootenay Lake, and the construction of dams. 

The construction of dikes eliminated flood-plain connectivity and related processes such as the deposition of 

4 Suspended-Sediment Transport, Kootenai River, Idaho
sediments onto the flood plain. The dikes increased confinement of streamflow to the river channel during floods, 

which resulted in increased stream energy and sediment 

transport during high flow, primarily prior to the closure of 

Libby Dam, because the dam greatly reduced high flows. 

Corra Lynn Dam, located at the outlet of Kootenay Lake 

(fig. 1), was completed in 1931. Corra Lynn Dam is 

operated for hydroelectric power and affects water levels in 

Kootenay Lake. The river channel above the dam at Grohman Narrows was deepened in 1939 in order to remove 

obstructions to free flow in the river and reduce hydraulic 

losses in the forebay of the dam (International Joint Commission, 1938, Order of Approval, Kootenay Lake, http://

www.ijc.org/conseil_ board/kootenay_lake/en/kootenay_ 

mandate_ mandat.htm). This allowed the lake to be kept at 

a lower level for dam operation, thus reducing the 

backwater effect in the Kootenai River. Construction of 

Libby Dam began in 1966, and Koocanusa Reservoir was 

officially impounded on March 21, 1972. Libby Dam is 

operated for flood protection, hydroelectric power, and 

recreational opportunities. 

The boundary between backwater and free-flowing 

water continually moves up and down the Kootenai River 

near Bonners Ferry in response to changes in Kootenay 

Lake elevations, inflow from tributaries between Bonners 

Ferry and Libby Dam, and releases from Libby Dam 

(fig. 3). Backwater conditions generally extend farther up 

the river as Kootenay Lake levels rise. Kootenay Lake 

levels generally are at a minimum during the autumn and 

winter months and at a maximum during the spring 

snowmelt runoff and the late spring and early summer 

releases from Libby Dam. 

Kootenay Lake levels and Kootenai River backwater 

conditions have changed over time. After the river channel 

at Grohman Narrows was deepened in 1939, lake level 

remained stable at an intermediate elevation for longer 

periods of the calendar year, probably in response to 

operation of Corra Lynn Dam (fig. 4). Seasonal fluctuations 

still occurred, but over a shorter period of time. Prior to 

Libby Dam, from 1940 to 1972, monthly median lake 

elevation ranged from 529.6 to 536.4 m, and the median 

elevation was 531.8 m. In 1948, West Kootenay Power and 

Light was granted, for a period of 5 years from autumn 1949 

RIVER DISTANCE, IN KILOMETERS

STAGE, IN METERS ABOVE SEA LEVEL

537.5

537.0

536.5

536.0

535.5

535.0

534.5

534.0

533.5

533.0

532.5

195 200 205 210 215 220 225 230 235 240 245 250 255

Figure 3. Generalized stage of the Kootenai River along three types of geomorphologic reaches from below the mouth of the

Moyie River to Copeland, Idaho. (Stage obtained from U.S. Geological Survey 1:24,000 quadrangle maps) Copeland Shorty Island Bonners Ferry

Mouth ofMoyie River

Meander reach

Buried gravel-cobble reach

Braided reach

 Backwater conditions occur in the meander

 reach and buried gravel-cobble reach and

 at times extend upstream to the very lower

 part of the braided reach

Description of Study Area 5
to spring 1954, an additional 0.6 m of storage above that 

approved in 1938 (Lynne Campo, West Kootenay Power 

and Light, written commun., 2000). From 1949 to 1954, the 

monthly median lake levels stabilized at a higher elevation 

of about 532.4 m. During the Libby Dam era from 1973 to 

1998, the monthly median lake elevation ranged from 529.9 

to 534.2 m and the median lake elevation was 531.6 m. 

Geology of the Kootenai River Basin

 The present geological and topographical characteristics of the Kootenai River Basin reflect the effects of 

massive glaciations during the Pleistocene Epoch, although 

in the white sturgeon spawning reach, bedrock is exposed 

near the bank of the river as far west as Mission Hill near 

Bonners Ferry (fig. 2A). The sills located just east of 

Bonners Ferry are the hardest geologic materials in the 

region (Kirkham and Ellis, 1926) and, therefore, the least 

eroded by glacial advances and retreats. 

During the Pleistocene Epoch, a lobe of the Canadian 

Cordilleran ice sheet repeatedly advanced down the Purcell 

Trench, filling the Kootenai River valley and mostly 

submerging the Purcell and Selkirk Mountains in northern 

Idaho. Ice finally left the valley about 10,000 years ago. 

During times when ice blocked the outlet of Kootenay Lake, 

a glacial lake formed in the Kootenai River valley and 

deposited a thick sequence of generally fine-grained lacustrine sediment consisting of clay and silt. Since the final 

glacial retreat and draining of glacial Kootenay Lake, the 

Kootenai River has incised and eroded some of the lacustrine clay-silt layer and deposited alluvial sediment onto 

the regional lacustrine clay-silt layer (Alden, 1953; Atwater, 

1986; Buchanan, 1989). The contact between the alluvial 

sand and the lacustrine clay-silt layer is a geologic unconformity. Distribution and thickness of glacial lacustrine 

clay-silt layers are, in part, functions of location in the 

Kootenai River, according to J-U-B Engineers (1998). Near 

Porthill, Idaho, drillers’ logs show thick clay-silt layers, 

some in excess of 610 m thick. In the upstream direction 

toward Bonners Ferry, these clay-silt layer units tend to 

become silty and thin, and near Bonners Ferry, the layers 

YEARS

WATER-LEVEL ELEVATION, IN METERS ABOVE THE

1928 GEODETIC SURVEY OF CANADA DATUM

537

536

535

534

533

532

531

530

529

1924 1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

Figure 4. Monthly median water levels on Kootenay Lake at Proctor (1924–30) and Queens Bay (1931–2000), British

Columbia, Canada. (Source of data is Environment Canada)

Proctor—1924 through 1930

Queens Bay—1931 through 2000

Monthly median water level

6 Suspended-Sediment Transport, Kootenai River, Idaho
become discontinuous. The regional lacustrine clay-silt 

layer is most often underlain by sand and gravel associated 

with Purcell Trench lobe retreats.

Lost Creek, Cascade Creek, and Myrtle Creek incise 

into alluvial fan deposits (fig. 2B and fig. 2C), according to 

erosion shift maps prepared by the U.S. Army Corps of 

Engineers (1983). Sediment resembling coarse-grained alluvial fan deposits has been identified in several wells near 

tributaries to the Kootenai River that drain either the Selkirk 

Mountains or the Purcell Mountains (J-U-B Engineers, 

1998).

Geomorphology of the Kootenai River 

Below Libby Dam

Snyder and Minshall (1996) classified three geomorphologic reaches in the Kootenai River between Libby Dam 

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

meander reach. The canyon reach is outside of the study 

area and extends from Libby Dam to 2 km below the mouth 

of the Moyie River. Here, the valley broadens and the river 

forms a braided reach as it courses over gravel and cobbles. 

This braided reach extends downstream into the study area 

(fig. 5) to a bedrock constriction near the U.S. 95 Bridge 

over the Kootenai River at Bonners Ferry. The meander 

reach extends from the bedrock constriction at Bonners 

Ferry, through the study area, and on to the confluence with 

Kootenay Lake. 

An additional geomorphological reach identified in 

the study area is a buried gravel-cobble reach. In this reach 

the gravel and cobble are buried with sand. The white sturgeon spawning habitat includes the braided reach and the 

buried gravel-cobble reach and principally lies within the 

meander reach.

The water-surface slope of the Kootenai River decreases at Bonners Ferry (fig. 3) and greatly influences the 

geomorphology of the white sturgeon spawning habitat. The 

braided reach of the Kootenai River extends from RKM 

256.2, which is 2.5 RKM downstream from the Moyie 

River, to RKM 245.75, which is about 0.25 RKM downstream from the U.S. 95 Bridge in Bonners Ferry (fig. 2A). 

The average water-surface slope in this reach is roughly 

0.00046. The braided reach has a relatively shallow water 

depth, typically less than 2 m during low flow. This reach 

consists mostly of gravel and cobble. White sturgeon have 

not been detected spawning in the braided river reach 

(Paragamian and others, 2002).

The buried gravel-cobble reach, RKM 245.75 to 

241.1, represents a transition zone between the higher 

gradient braided reach and the lower gradient meander reach 

(fig. 2A and fig. 3). This reach is relatively straight and 

stable, with no evidence of the rapid channel shifting 

observed in the braided reach. The straightness and stability 

of the channel may be controlled by an outcrop of bedrock 

near the river channel between the U.S. 95 Bridge and 

Mission Hill (fig. 2A). The water-surface slope in this reach 

is about 0.00017, less than one-half the gradient in the 

braided reach. Water depths in the buried gravel-cobble 

reach are deeper than in the braided reach and typically 

range from 3 to 6 m. Sand overlies most of the discontinuous cobble and gravel deposits along this reach.

The meander reach (fig. 5) is between RKM 241.1, 

downstream from Bonners Ferry near the confluence of 

Deep Creek, and Kootenay Lake. The Kootenai River gently 

bends north and begins meandering at about RKM 241.1. 

The average water-surface slope is roughly 0.00002 in the 

meander reach between RKM 199.5 to 241.1, about onetenth the gradient in the buried gravel-cobble reach. Water 

depths in the meander reach exceed 12 m in the thalweg. 

Fluvial sand occurs throughout most of the meander reach. 

A reconnaissance seismic survey (Barton, 1998) found that 

the fluvial sand forms dunes throughout the buried gravelcobble reach and the meander reach, including areas used by 

sturgeon for spawning (fig. 6). The Pleistocene lacustrine 

clay-silt layer forms the river substrate in parts of the thalweg. Prior to European settlement, the valley bottom consisted of wide flood plains, wetlands, and riparian forest. 

Subsequently, natural levees and sloughs were replaced with 

constructed dikes to contain overbank flow, and wetlands 

were drained and developed into annual and pasture croplands (Pacific Watershed Institute and Resources, 1999).

STUDY METHODS

The approach to meeting the objectives of the study 

was threefold: analysis of sediment transport, analysis of 

channel geometry, and mapping of channel substrate. Analysis of sediment transport and channel geometry was based 

on data previously collected by the USGS.

Measuring Streamflow and the Concentration of Suspended Sediment

Suspended sediment is the sediment that at any given 

time is maintained in suspension as a colloid or by the 

upward components of turbulent currents. Suspendedsediment concentration is the velocity-weighted mean 

concentration of suspended sediment in a sampling zone 

from the water surface to a point approximately 0.1 m above 

the bed, expressed as milligrams of dry sediment per liter of 

water-sediment mixture (mg/L). Suspended-sediment load, 

reported as metric tons per day (mt/d), is the rate at which 

the dry weight of sediment passes a section of a stream in a 

given time. Depth-integrated techniques are used to define 

Study Methods 7
the sediment concentration at vertical transit points in a river 

cross section. The suspended-sediment concentration over 

the cross section is determined from depth-integrated 

measurements at vertical transit points. Daily monitoring of 

suspended sediment is provided by samples collected at a 

fixed point which are related to sediment concentration over 

the cross section with empirical coefficients. Additional 

information about USGS suspended-sediment sampling 

techniques can be found in Edwards and Glysson (1999).

The inactive USGS streamflow-gaging station 

12318500 at Copeland, Idaho (fig. 5), is the only suspendedsediment station near the present white sturgeon spawning 

reach. This gage is located 15 RKM downstream from the 

white sturgeon spawning reach. Suspended-sediment samples were collected daily from 1966 to 1983, and the data 

reside in the USGS National Water Inventory System 

(NWIS) database. Three samples from 1968 to 1970 and 

four samples from 1974 to 1976 were analyzed for particlesize distribution by 1

/2 Phi classes using the visualaccumulation tube methods. Particle-size distribution is 

reported as diameter, in millimeters, by 1/2 Phi class sizes: 

0–0.002, 0.002–0.004, 0.004–0.008, 0.008–0.016, 0.016–

0.031, 0.031–0.062, 0.062–0.125, 0.125–0.25, and 0.25–0.5 

millimeters. For the 1974–76 samples, class sizes 0.062–0.5 

were determined using the wet sieve method.

Suspended-sediment load was measured periodically 

at three USGS streamflow-gaging stations. Station 

12301933 was measured from May 1968 to June 1971 and 

from May 1999 to July 2000. This gaging station is located 

on the Kootenai River about 28 km below Libby Dam in 

Libby, Montana (fig. 1). The Fisher River and Libby, Rainy, 

and Alexander Creeks flow into the Kootenai River between 

this gaging station and Libby Dam. Station 12304500 was 

measured from May through August 1999. This gage is 

located on the Yaak River about 0.5 km upstream from its 

mouth at the Kootenai River (fig. 1). The Yaak River enters 

the Kootenai River just east of the Idaho-Montana border 

below Kootenai Falls: this unregulated tributary drains a 

1,226-km2 basin and has an annual mean daily flow of 

20 m3/s for 1956–99. Station 12302055 was measured from 

April 1969 to December 1975 and from May 1999 to July 

2000. This gaging station is located on the Fisher River 

about 1.3 km upstream from its mouth at the Kootenai River 

(fig. 1). The Fisher River enters the Kootenai River just 

below Libby Dam; this unregulated tributary drains a 1,341-

km2 basin and has an annual mean daily flow of 20 m3/s.

River Channel Geometry Computation

The streamflow-gaging station nearest the present 

white sturgeon spawning reach is the Copeland gage on the 

Kootenai River (fig. 1). Stream-discharge measurements, 

which included information about river geometry, were 

made from 1929 to 1993 from a permanent cableway that 

crosses the river at Copeland, Idaho. The river stage, depth, 

and other data recorded along this cross section were 

measured in relation to permanent benchmarks. Measurement interval was typically about 6 weeks. Data of this type 

are extremely reliable in analyzing changes in river geometry over time since they are repeatedly obtained from the 

same location.

Data from the Copeland gage such as discharge, 

average velocity, river stage, cross-sectional area of the 

river, and river width reside in the USGS NWIS database. 

Channel cross-section elevation data and thalweg data at the 

Copeland gaging station are not stored in the NWIS database but were compiled for analysis from archived notes 

made by USGS personnel while measuring discharge at the 

gaging station. USGS level notes for the Copeland gaging 

station, retrieved from Federal archives, indicate that the 

datum for this gaging station typically was resurveyed once 

a year to verify the accuracy of river-stage measurements. 

These level notes were reviewed to insure that any changes 

to the gage datum were (1) correctly entered into the NWIS 

database and (2) correctly applied to the channel crosssection elevation data and thalweg data compiled from 

archived field records.

 Mean riverbed elevation was computed by subtracting the mean river depth from river stage at the time of 

the discharge measurement. The mean river depth was 

computed by dividing the cross-sectional area of the river by 

the water-surface width. The river stage is calculated as 

gage height plus stream-gage datum elevation. Thalweg 

elevation was computed by subtracting the thalweg depth 

from the river stage at the time of the discharge measurement. Thalweg depth is not stored in the NWIS database but 

was computed by subtracting the maximum depth along the 

river cross section that was recorded on the discharge 

measurement note from the river stage at the time of the 

discharge measurement. The riverbed elevation was computed by subtracting river depth from river stage at the time 

of the discharge measurement. Depth values are relative to 

water-surface elevation.

Mapping of Channel Substrate

The description of the channel substrate—lacustrine 

clay-silt layer and alluvial deposits—in the white sturgeon 

spawning reach of the Kootenai River is based on seismic 

subbottom profiles, sediment cores, and ponar dredge samples of the riverbed. Locations of seismic subbottom profiles 

and sediment-coring sites are shown on figure 2. 

SEISMIC SUBBOTTOM PROFILING

Seismic subbottom profiles were made at various 

cross-section locations in the study area from RKM 244.3 to 

8 Suspended-Sediment Transport, Kootenai River, Idaho
USGS 

identifier Date

Latitude

(degrees, 

minutes, 

seconds)

Longitude

(degrees, 

minutes, 

seconds)

River 

kilometer

Sediment 

core type

Depth core 

penetrated, 

in meters

Core 

recovery, 

in meters

Water 

depth, 

in 

meters

Type of 

sediment

K3-TH 9/21/00 48 47.301 116 23.703 228.5 VC 3.5 2.1 7.9 AL No

K3-C 9/21/00 48 47.346 116 23.707 228.5 VC 3.5 2.0 4.9 AL No

K5-C 9/21/00 48 46.546 116 23.423 229.5 VC 3.2 2.5 7.3 AL, LU No

K5-TH 9/21/00 48 46.568 116 23.392 229.5 VC 3.5 2.0 8.5 LU No

K6-RB 9/21/00 48 45.873 116 23.179 230.9 VC 3.5 3.4 6.1 AL No

K6-TH 9/21/00 48 45.880 116 23.202 230.9 VC 3.5 2.7 14.9 AL, LU No

K6-LB 9/21/00 48 45.865 116 23.221 230.9 VC 3.5 1.9 9.8 AL No

K6.5-C 9/21/00 48 45.416 116 23.750 232.0 VC 3.3 0.8 3.7 AL No

K9-LB 9/19/00 48 44.831 116 24.852 233.8 PC 0.3 0.3 5.1 AL No

K9-C 9/19/00 48 44.84 116 24.851 233.8 PC 0.6 0.4 5.2 AL No

K9-RB 9/20/00 48 44.837 116 24.771 233.8 VC 1.3 1.3 4.2 AL No

K9.5-TH 9/20/00 48 44.611 116 24.935 234.3 VC 0.2 0.0 12.5 AL Yes

K9.5-C 9/20/00 48 44.595 116 24.915 234.3 VC 0.3 0.3 10.2 AL Yes

K9.5-RB 9/20/00 48 44.597 116 24.901 234.3 VC 3.5 1.9 6.9 AL No

K10-RC 9/20/00 48 44.406 116 24.833 234.5 VC 3.5 0.8 7.3 AL No

K10-TH1 9/19/00 48 44.375 116 24.885 234.5 PC 0.1 0.0 8.4 AL Yes

K10-TH2 9/19/00 48 44.379 116 24.881 234.5 PC 0.8 0.3 12.8 AL Yes

K10-RTH 9/20/00 48 44.382 116 24.879 234.5 VC 3.5 2.0 8.4 AL No

K11-C 9/20/00 48 44.358 116.24.300 235.1 VC 3.5 1.9 4.7 AL No

K11-LB 9/20/00 48 44.333 116 24.319 235.1 VC 3.5 2.1 3.7 AL No

K12-TH1 9/20/00 48 44.559 116 23.607 236.1 VC 3.5 1.9 13.7 AL Yes

K12-TH2 9/22/00 48 44.469 116 23.580 236.1 VC 2.9 1.4 13.1 AL Yes

K12-LB 9/22/00 48 44.450 116 23.590 236.1 VC 3.5 2.0 8.5 AL, LU No

K13-LB1 9/20/00 48 44.105 116 22.993 237.1 VC 3.5 1.8 6.1 AL No

K13-LB2 9/20/00 48 44.102 116 23.005 237.1 VC 3.5 1.3 2.9 AL No

K13-RB 9/19/00 48 44.121 116 22.941 237.1 PC 0.0 0.4 5.9 AL, LU No

K13-TH 9/20/00 48 44.113 116 22.965 237.1 VC 3.5 3.4 11.9 LU No

K14-TH 9/22/00 48 43.719 116 23.282 237.9 VC 2.0 0.6 6.6 AL, LU No

K15.5-TH 9/22/00 48 43.125 116 23.471 239.0 VC 3.5 2.1 8.8 AL, LU Yes

K16-C1 7/22/00 48 42.815 116 23.335 239.7 VC 0.6 0.6 5.6 AL No

K16-C2 9/22/00 48 42.814 116 23.340 239.7 VC 3.1 2.1 5.6 AL No

K16-LB 9/22/00 48 42.798 116 23.360 239.7 VC 3.5 3.4 4.6 LU No

K18-LB 9/22/00 48 42.240 116 21.881 241.6 VC 3.5 2.2 5.5 AL, LU No

K18-TH 9/22/00 48 42.261 116 21.871 241.6 VC 2.3 1.6 5.5 AL, LU Yes

K20-TH 9/22/00 48 41.807 116 20.221 243.9 VC 1.5 0.6 4.6 AL Yes

Table 1. Sediment cores of the Kootenai River bed near Bonners Ferry, Idaho, October 19–22, 2000

Core 

contains 

sediment 

coarser 

than sand

[Geologist logs presented in figure 24; C, near center of river; TH, thalweg; LB, near left bank; RB, near right bank, 

RTH, right of thalweg; VC, vibracore; PC, piston core; core recovery, does not include a thickness correction for 

compaction of sand due to vibratory movement; AL, Alluvial; LU, Lacustrine clay and silt; flow at Bonners Ferry was 

227 cubic meters per second]

Table 1 9
226 using a seismic system from the USGS Branch of 

Geophysical Operations and Support, Stoors Mansfield, 

Connecticut (fig. 7). Seismic subbottom profiling 

methodology is described in detail in Haeni (1986). This 

system transmits swept FM waveforms that operate between 

0.5 and 2.0 kHz (kilohertz). A 0.2-mt tow vehicle that 

transmits and receives the FM signal was pulled behind the 

survey boat in the water. During surveying operations, the 

boat was propelled at 2–3 km per hour, the sound source 

was fired every 0.5 second, and a continuous record of the 

subsurface was obtained. The unprocessed data were digitally recorded to allow for post-data acquisition processing. 

Spatial referencing of seismic subbottom profiles was 

accomplished using a Global Positioning System (GPS).

The seismic-acoustic signals displayed on subbottom 

profiles show the interface between different layers of sediment below the riverbed. The interface of the profiles is 

referred to as a subsurface reflector. Depths of subsurface 

reflectors were calculated assuming an acoustic velocity of 

1,524 m per second. Depth of geophysical exploration 

corresponds to the deepest seismic reflector and ranged 

from less than 1 m to greater than 10 m below the riverbed. 

Some natural, coarse-grained subsurface materials that limit 

depth of exploration caused the variation in depth of exploration. Seismic resolution, the ability to identify the 

contact between different layers, is on the order of 0.2 m or 

greater. Ghost reflectors representing seismic ringing in the 

water column between the free-water surface and riverbed 

are present on many subbottom profiles. 

CORING OF RIVERBED SEDIMENT

Thirty-five cores of riverbed sediment were collected 

from RKM 243.9 to 225.8 in the study area (table 1; see 

fig. 2 for locations). A 7.3-m pontoon coring boat was 

employed for taking vibracores and piston cores of sediment 

beneath the riverbed (fig. 8). Sites for instream sediment 

cores were not evenly distributed throughout the study area 

but were concentrated in the spawning reaches. The core 

sites were referenced spatially using GPS. The 35 sediment 

cores were taken at or near cross sections of the river where 

seismic subbottom profiles were obtained. Generally, one 

core was taken from the deepest part of the thalweg where 

erosion may occur and another in shallower water where 

deposition may occur. At eight cross sections, two or three 

cores were taken in shallower water. Thirty cores were 

collected using the vibracoring system and five cores were 

collected using a piston coring system. The vibracoring 

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

is 3.66 m in length and capable of recovering the clay-silt 

layer, silt, sand, gravel, and some cobble. The maximum 

length of core recovered during data collection was 3.5 m, 

with an average recovery of 3.0 m. Twenty-two vibracores 

sampled 3 to 3.5 m of the channel substrate. The piston 

coring system is equipped with a 0.08-m-diameter core 

barrel that is 1.52 m in length. The maximum recovery for 

the piston core was 0.8 m and the average recovery was 

0.6 m. 

The vibrating action of the vibracore greatly enhanced 

penetration of the core barrel into the substrate. However, 

the vibrating action caused compaction of sand and organic 

debris (no effect on clay-silt layers) in the core barrel. Compaction of sand in vibracores has been observed in other 

settings (Keith Ludwig, U.S. Geological Survey, oral 

commun., 2000). Thickness of sand and organic layers in 

vibracores was adjusted for compaction by multiplying 

measured thickness by a correction factor. The thickness 

correction factor was determined from layer thickness penetrated by the vibracore divided by the thickness of sand or 

organic material recovered in the core barrel. Calculations 

were adjusted to account for any silt or clay layer(s) recovered in the core. The average correction factor was about 

1.6. 

The Kootenai Tribe of Idaho collected bed material 

samples from the Kootenai River on June 20, 2000, between 

RKM 226 and 244.3. These samples were taken with a 

ponar dredge sampler at 22 sites located near mid-channel 

and near the riverbanks (table 2).

LIMITATIONS ON MAPPING CHANNEL 

SUBSTRATE

Because of the limited resolution of seismic 

subbottom profiles and a limited number and distribution of 

sediment cores, the contact lines defining the composition of 

the river substrate are general delineations and are inferred 

in most cases. Seismic reflectors on subbottom profiles do 

not always indicate a specific type of sediment layer, but 

may indicate only the boundary between two adjacent layers 

of sediment. Thus, cores of riverbed sediment or other 

“ground truth” are required to correctly interpret the sediment texture of seismic reflectors displayed on subbottom 

profiles. Only three riverbed sediment cores were collected 

in the buried gravel-cobble reach near Bonners Ferry, RKM 

245.75 to 241. Current understanding of the lateral extent, 

thickness, and particle-size distribution of the buried gravelcobble layers is generalized. Additional cores of the riverbed are needed in this reach in order to construct a more 

detailed map that shows the lateral extent, thickness, and 

particle-size distribution of the buried gravel-cobble layers.

CHANGES IN STREAMFLOW AND 

SUSPENDED-SEDIMENT REGIMES

Analysis of streamflow and suspended-sediment 

regimes for the Kootenai River is based largely on the 

period of record at the Copeland gage that includes both 

stream-flow and suspended-sediment load from 1966 to 

1983 (fig. 9). Streamflow for the gage at Porthill 

(12322000) also is used in the analysis (fig. 10) because this 

10 Suspended-Sediment Transport, Kootenai River, Idaho
gage, unlike the Copeland gage, was operational throughout 

the 1980s and 1990s and, hence, provides an account of 

streamflow con-ditions during that period of time. 

Streamflow at Porthill is slightly greater than at Copeland 

owing to a larger drainage area.

Streamflow

On the basis of records for the Copeland gage from 

1966 to 1971, the streamflow regime for the Kootenai River 

during the pre-Libby Dam era was characterized by peak

flows resulting from spring snowmelt occurring from late 

April through mid-July (fig. 9A). Annual median peak 

spring-summer runoff flow was about 2,237 m3

/s, with a 

slow recession of flow generally starting in mid-June and 

reaching base-flow conditions in September. The remaining 

months had stable base-flow conditions with occasional 

smaller peaks caused by infrequent storms including rainon-snow events. The annual median base flow during the 

months of October through February was 88 m3/s. 

From 1966 to 1971, the average cross-sectional 

streamflow velocity during 62 measurements at the Copeland gage ranged from 0.06 to 1.21 m/s (fig. 11). During 

1929–1971, the period of record at the Copeland gage for 

the pre-Libby Dam era, the maximum average crosssectional streamflow velocity and flow among the 600 measurements were 1.34 m/s and 3,115 m3/s on May 28, 1961. 

Although one of the principal effects of Libby Dam is a 

decrease in the range of daily mean flows, the annual daily 

mean flow was nearly identical after the closure of Libby 

Dam, based on the period of record at the Porthill gage 

(fig. 10). The annual daily mean flow from 1929 to 1971 

was 469 m3

/s, compared with 454 m3/s from 1973 to 2000.

On the basis of the records for the Copeland gage 

from 1973 to 1983, the streamflow regime for the Kootenai 

River for the Libby Dam era was characterized by daily 

median flows that peaked at about 600 m3

/s (fig. 9B). Peak 

flows generally occurred twice a year, during the winter and 

during the spring and early summer (fig. 9B). Median daily 

spring-summer runoff streamflow during the Libby Dam era 

was several times less than during the pre-Libby Dam era 

(fig. 9A and fig. 9B). During the fall and winter months, the 

annual median daily flows fluctuated much more than 

during the pre-Libby Dam era (fig. 9A and fig. 9B). Long 

periods of sustained higher flows occurred during the fall 

and winter of the Libby Dam era, reflecting hydroelectric 

power generation when electrical demand is greatest in this 

area. The average cross-sectional streamflow velocity from 

83 measurements at the Copeland gage ranged from 0.11 to 

0.8 m/s (fig. 11). The maximum average cross-sectional 

streamflow velocity during the Libby Dam era was about 

three-fifths that during the pre-Libby Dam era. 

Beginning in 1991, Kootenai River flows were 

augmented with additional release of water from Libby Dam 

during white sturgeon spawning in May and June in an 

attempt to help resume recruitment; however, the augmented flow is much less than pre-Dam peak flows. Since 

1995, flows in the Kootenai River during white sturgeon 

spawning have been higher with the additional release of 

water from Libby Dam. The augmented streamflow is 

Table 2. Sediment samples of Kootenai River bed taken with ponar dredge sampler on June 20, 2000. 

(Samples collected by the Kootenai Tribe of Idaho.)

[Streamflow at Bonners Ferry was about 708 cubic meters per second.]

Water depth at dredging location

in meters

Near right Near left

River kilometer Mid-channel bank bank General lithologic description

244.3 15.2 8.2 Fine- to coarse-grained alluvial sand

243 6.7 7.9 Fine- to coarse-grained alluvial sand

241 8.2 7.3 Fine- to coarse-grained alluvial sand

239.8 7.9 7.0 Fine- to coarse-grained alluvial sand

237.5 7.9 9.4 Fine- to coarse-grained alluvial sand

234.5 7.6 9.8 Fine- to coarse-grained alluvial sand

323 6.7 9.8 Fine- to coarse-grained alluvial sand

231.5 5.5 7.0 Fine- to coarse-grained alluvial sand

230.3 9.1 6.7 Fine- to coarse-grained alluvial sand

229.5 8.8 4.0 Fine- to coarse-grained alluvial sand

226 6.7 3.7 Fine- to coarse-grained alluvial sand

Changes in Streamflow and Suspended-Sediment Regimes 11
YEARS

STREAMFLOW, IN CUBIC METERS PER SECOND

4,000

3,500

3,000

2,500

2,000

1,500

1,000

500

0

1929 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

Figure 10. Streamflow at U.S. Geological Survey streamflow-gaging station 12322000 on the Kootenai River at Porthill, Idaho,

1929–2000.

Annual daily mean streamflow

Daily mean streamflow

Libby Dam closure

INSTANTANEOUS STREAM DISCHARGE MEASURED

AT CABLEWAY, IN CUBIC METERS PER SECOND

AVERAGE FLOW VELOCITY MEASURED AT

CABLEWAY, IN METERS PER SECOND

1.5

1.2

0.9

0.6

0.3

0

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

Figure 11. Relation between stream discharge and streamflow velocity at U.S. Geological Survey streamflow-gaging station

12318500 on the Kootenai River at Copeland, Idaho, 1929–93.

Pre-Libby Dam era—1929–65

Pre-Libby Dam era and daily suspended-

 sediment sampling—1966–71

Libby Dam era and daily suspended-

 sediment sampling—1973–83

Libby Dam era—1984–93

12 Suspended-Sediment Transport, Kootenai River, Idaho
roughly one-half the peak streamflow during the pre-Libby 

Dam era. 

Lipscomb and others (1997) conducted an Acoustic 

Doppler Current Profiler survey on June 11 and 12, 1997, 

under augmented streamflows of 1,240 and 1,260 m3

/s. This 

survey measured streamflow velocities in the white sturgeon 

spawning reach at three 500-m reaches. The average streamflow velocity calculated for each reach at a depth of 6.8 m 

ranged from 0.53 to 0.89 m/s (Lipscomb and others, 1997, 

table 1). These velocities are lower than the velocities 

observed at the Copeland gage during snowmelt runoff, 

when peak discharge exceeded 1,500 m3

/s most years, 

during the pre-Libby Dam era.

Suspended-Sediment Regime

In the white sturgeon spawning reach, transport of the 

abundant sand is controlled by streamflow. The sources of 

sand since the closure of Libby Dam in the white sturgeon 

spawning reach are Deep Creek, Myrtle Creek, and erosion 

of the riverbanks, but mainly upstream sources, including 

tributaries and the bed of the Kootenai River below Libby 

Dam.

During snowmelt runoff in the pre-Libby Dam era, 

the data collected at the USGS gage at Copeland (fig. 9A

and fig. 12) indicate that large amounts of suspended sediment were transported through the white sturgeon spawning 

reach. The annual suspended-sediment load transported 

through the Kootenai River white sturgeon spawning reach 

(fig. 9C) decreased by a factor of 6 after the closure of 

Libby Dam in 1972: mean annual pre-Libby Dam load 

(1966–71) was 1,743,900 mt, whereas the dam-era load 

(1973–83) was 287,500 mt. Annual median daily load 

during the pre-Libby Dam era ranged from 13 mt/d at 

114 m3/s to 48,700 mt/d at 2,135 m3

/s, and during the Libby 

Dam era from 53 mt/d at 199 m3

/s to 1,560 mt/d at 

581 m3/s. Suspended-sediment transport during the Libby 

Dam era was minimal, about 16 percent of the pre-Libby 

Dam era amount. 

The magnitude of Kootenai River flows that occur 

less than 10 percent of the time has been significantly decreased since closure of Libby Dam; therefore, the capacity 

of the river to transport suspended sediment has been greatly 

DURATION OF STREAMFLOW, PERCENT TIME

STREAMFLOW, IN CUBIC METERS PER SECOND

4,000

3,500

3,000

2,500

2,000

1,500

1,000

500

0

0.001 0.01 0.1 1 10 100

Figure 13. Comparison of the duration for daily mean flows during the pre-Libby Dam era and Libby Dam era at U.S. Geological

Survey streamflow-gaging station 12322000 on the Kootenai River at Porthill, Idaho, 1929–2000.

Pre-Libby Dam era—1929–71

Libby Dam era—1973–94

Libby Dam era with consistent

 flow augmentation for sturgeon

 spawning—1995–2000

Changes in Streamflow and Suspended-Sediment Regimes 13
reduced. In general, streamflow equaled or exceeded less 

than 10 percent of the time usually transports a majority of 

the annual sediment load (Wolman and Miller, 1960); moreover, the increment of discharge that transports the largest 

quantity of sediment over a period of years is equaled or 

exceeded less than 3 percent of the time (Andrews, 1986). 

During the pre-Libby Dam era, daily mean flow exceeded 

1,242 m3

/s fewer than 37 days per year. Daily mean flow 

exceeded 1,242 m3/s fewer than 3 days per year during the 

Libby Dam era from 1973 to 1994, and 10 days per year 

during the Libby Dam era from 1995 to 2000 with consistent flow augmentation from Libby Dam for white sturgeon spawning. In addition, during the pre-Libby Dam era, 

flows exceeded 3,230 m3/s almost 11 days per year; flows 

have not exceeded 1,739 m3/s during the Libby Dam era 

(fig. 13). 

Suspended sediment is being trapped behind Libby 

Dam that otherwise was transported downstream from the 

upper part of the river basin during the pre-Libby Dam era. 

On the basis of periodic suspended-sediment samples 

collected at the USGS gaging station 12301933 below 

Libby Dam at Libby, Montana, the median suspendedsediment concentration during the pre-Libby Dam era was 

337 mg/L (measured during eight sampling events between 

May 27, 1968, and June 1, 1971) and, during the Libby Dam 

era, the concentration was 2 mg/L (measured during seven 

sampling events between May 19, 1999, and June 27, 2000) 

(fig. 12A). On the basis of these samples and on streamflow, 

the median daily suspended-sediment load at Libby, 

Montana, during the pre-Libby Dam era was 39,400 mt/d 

and, during the Libby Dam era, the load was 39 mt/d 

(fig. 12B).

During periods of high flow in tributaries between 

Bonners Ferry and Libby Dam, the water flowing out of 

Libby Dam is likely a much smaller source of suspended 

sediment to the Kootenai River than are its tributaries. 

During periods of low flow in tributaries, the water flowing 

out of Libby Dam is a larger source of suspended sediment 

to the Kootenai River than are its tributaries. Tributary additions of suspended sediment to the Kootenai River between the white sturgeon spawning reach near Bonners 

Ferry and Libby Dam have been measured only during the 

Libby Dam era and only for two tributaries, Yaak River and 

Fisher Creek. Suspended-sediment load was measured 

during four sampling events on the Yaak River from May to 

August 1999 at USGS gage 12304500. The load ranged 

from 0.7 mt/d with a flow of 8 m3/s on August 17 to 1,370 

mt/d with a flow of 202 m3/s on May 25. For comparison, 

during roughly the same period, measurements taken at 

USGS gage 12301933 below Libby Dam show the median 

daily load was 39 mt/d during spring snowmelt runoff, on 

the basis of six sampling events between May 19, 1999, and 

June 27, 2000 (fig. 12B). 

Hysteresis Effect on Transport of 

Suspended Sediment

In the pre-Libby Dam era, suspended-sediment 

concentrations at the Copeland gage during first flush (the 

sudden and dramatic increase in streamflow near the start of 

the snowmelt runoff period after months of low flow) were 

about two to three times higher than concentrations 

measured at similar streamflow later in the runoff season. 

This hysteresis effect on sediment transport is characteristic 

of streams with large variation in flows. For example, 

suspended-sediment concentrations ranged from about 400 

mg/L to 600 mg/L on 3 days during first-flush events in 

1967 (fig. 14A). More important is that the sediment 

concentrations subsequent to the first flush are lower (150–

350 mg/L) even though the flows are still elevated. Prior to 

these first-flush events, the suspended-sediment 

concentrations were less than 20 mg/L. This hysteresis 

effect can be further explored by studying the median daily 

suspended-sediment load during the pre-Libby Dam era 

from about April 30 to June 6 on the rising limb of the 

hydrograph and during June 7 to July 25 on the falling limb 

of the hydrograph (fig. 9A). During the April 30 to June 6 

period, the volume of suspended sediment transported 

through the white sturgeon spawning habitat and past the 

Copeland gage was roughly 24 percent greater on the rising 

limb of the hydrograph than on the falling limb. 

Furthermore, the volume of streamflow through the white 

sturgeon spawning habitat was roughly 10 percent less on 

the rising limb of the hydrograph than on the falling limb.

In the Libby Dam era, some data also show a 

hysteresis effect for sediment transport. During the period of 

record for the Libby Dam era, the only significant first-flush 

event occurred in 1974. Suspended-sediment concentrations 

at the beginning of the first-flush event in April ranged from 

200 to 300 mg/L for 3 days (fig. 14B) and concentrations 

quickly decreased, although streamflow remained high. 

During 1978 and 1983, the maximum suspended-sediment 

concentrations (fig. 14B) were less than 55 mg/L.

Suspended-Sediment Transport During 

the 1974 White Sturgeon Recruitment

The 1974-year class of wild sturgeon is the progeny 

of the most recent successful white sturgeon recruitment. 

Although the Kootenai River white sturgeon have 

apparently spawned on a yearly basis since 1974, these 

spawning events have failed to produce new generations of 

white sturgeon (Vaughn Paragamian, Idaho Department of 

Fish and Game, written commun., 2000). During the period 

of suspended-sediment record for the Libby Dam era (1973–

83), the only notable transport of suspended sediment 

14 Suspended-Sediment Transport, Kootenai River, Idaho
occurred prior to and during the 1974 spawning recruitment 

event. 

Prior to the spring-summer 1974 white sturgeon 

recruitment event, a large, warm-rain-on-snow event took 

place during January 15–17, 1974 (fig. 14B). On January 

17, the Fisher River, 5.6 RKM downstream from Libby 

Dam, produced 56,900 mt/d of suspended sediment at flows 

of 186 m3

/s. The load that moved past the Copeland gage 

was 5,940 mt/d at 1,090 m3/s on January 18. The sediment 

load data for the Fisher River gage on January 17 and for 

the Copeland gage on January 18 are compared because a 

particle of water requires roughly 0.7 day of traveling between the two sites on the Kootenai River; the amount of 

time needed is a function of streamflow and backwater 

conditions. During the period January 15–20, about 175,900 

mt of suspended sediment moved past the Fisher River gage 

at a 6-day mean flow of 120 m3/s, whereas about 105,600 

mt of suspended sediment moved past the Copeland gage at 

a 6-day mean flow of 1,040 m3

/s. A minimum of 70,300 mt 

of sediment was deposited onto the bottom of the Kootenai 

River between the two sites. Because this computation does 

not include the sediment loads from other tributaries, the 

amount of sediment deposited is greater than 70,300 mt. The 

loads from other tributaries were not measured.

During the period of suspended-sediment record for 

the Libby Dam era, the only notable multiweek suspendedsediment transport event with streamflow that approached 

pre-Libby Dam conditions took place from April 24 to July 

5, 1974 (fig. 14B), during the white sturgeon spawning 

season. Daily mean streamflow ranged from approximately 

736 to 1,416 m3

/s. During May 5–24, flows ranged from 

736 to 850 m3

/s. Daily mean flows exceeded 850 m3/s for 

53 days during the 73-day period. The peak flushing flow 

occurred on April 27. The sediment load peaked at 24,500 

mt/d with a mean daily flow of 1,266 m3/s, and sediment 

concentration peaked at 265 mg/L. During this period, there 

were 20 days when loads were greater than 9,070 mt/d. This 

event represents roughly an order-of-magnitude increase in 

sediment transport over the median daily load during the 

period of suspended-sediment record for the Libby Dam era. 

Immediately after dam construction, the sudden change in 

river hydraulics meant that sediment transport, including the 

aggradation and degradation of the river bottom, was in the 

process of shifting to a new equilibrium. Thus, sediment 

transport conditions in the river might be unique and not 

representative of conditions during either the pre-Libby 

Dam or Libby Dam era.

PARTICLE DIAMETER, IN MILLIMETERS

PERCENT FINER

100

90

80

70

60

50

40

30

20

10

0

0.002 0.004 0.008 0.016 0.031 0.062 0.125 0.25 0.5

Figure 15. Distribution of particle size in suspended-sediment samples collected at U.S. Geological Survey streamflowgaging station 12318500 on the Kootenai River at Copeland, Idaho, 1968–76.

Clay Sand

5 June 1968

8 June 1969

5 June 1970

30 May 1974

17 June 1974

26 May 1976

30 May 1976

2,133

2,331

1,685

1,113

1,388

470

1,994

DATE STREAMFLOW, in

cubic feet per second

--------

--------

--------

--------

--------

--------

--------

Sediment diameters were determined using

the visual-accumulation tube: Note the

0.062–0.5 size classes for 1974–76 were

determined using wet sieve method

Changes in Streamflow and Suspended-Sediment Regime 15
Suspended-Sediment Particle Size

On the basis of limited particle-size analyses 

performed on samples collected at the Copeland gage, the 

percentage of sand in three of the four suspended-sediment 

samples collected during spring and early summer high 

flows during the Libby Dam era appears to be less than the 

percentage in three samples collected during the pre-Libby 

Dam era (fig. 15). The 1

/2 Phi particle-size data are limited 

to three suspended-sediment samples collected during 

1968–70 at flows ranging from 1,685 to 2,331 m3/s and to 

four samples collected during 1974–76 at flows ranging 

from 470 to 1,388 m3/s. The wash load, silt and clay that are 

suspended in the water column and found in relatively 

small quantities in the alluvial substrate, is a greater 

percentage of the overall suspended-sediment load during 

the Libby Dam era. Stream velocity does not affect wash 

load but does affect the transport of sand. 

CHANGES IN CHANNEL GEOMETRY AND 

SUBSTRATE

Changes in the geometry and composition of the 

channel substrate in the white sturgeon spawning reach of 

the Kootenai River after closure of Libby Dam were 

determined by assessing historical gaging-station data and 

seismic subbottom profiles and sediment core samples of 

the riverbed. There are no streamflow gages located in the 

white sturgeon spawning reach, but data from the Copeland 

gage were used as a surrogate to describe changes in channel geometry in the spawning reach because conditions at 

the Copeland gage are similar to those in the spawning 

reach: both are located in the meander reach and in 

backwater. The degree to which the fluctuation of channel 

substrate at Copeland could be compared with that in the 

spawning reach could not be determined.

Channel Geometry

The channel geometry was evaluated for the period of 

record at the Copeland gage, 1929 to 1993. The effect of 

changing flow regulation at Libby Dam on channel 

geometry during the mid- and late 1990s could not be 

evaluated because the gage was deactivated in 1994. The 

Copeland gage is located 15 RKM downstream from the 

white sturgeon spawning reach (see fig. 5 for location). The 

Kootenai River at the Copeland gage flows toward the 

northwest. Beneath the cableway near the toe of the right 

bank, the riverbed is roughly 3 to 5 m deeper than the 

riverbed near the toe of the left bank. The thalweg generally 

is formed near the toe of the right bank; however, there have 

STREAMFLOW, IN CUBIC METERS PER SECOND

ELEVATION OF RIVERBED AT THALWEG, IN METERS

523

522

521

520

519

0 500 1,000 1,500 2,000 2,500 3,000

Figure 17. Fluctuation of minimum riverbed elevation with streamflow for the pre-Libby Dam and Libby Dam eras on the

Kootenai River beneath the stationary cableway at U.S. Geological Survey streamflow-gaging station 12318500 at

Copeland, Idaho, 1929–93.

Pre-Libby Dam era—1929–71

Libby Dam era—1973–93

16 Suspended-Sediment Transport, Kootenai River, Idaho
been periods where a thalweg forms in the center of the 

channel. 

CHANNEL WIDTH AND MIGRATION

A somewhat subtle change during the Libby Dam era 

was an increase in channel migration. On the basis of the 

entire record of stream-gaging discharge measurements, the 

median river width was 147 m for both the pre-Libby Dam 

era (1929–71) and the Libby Dam era (1973–93). The 

average river width was 149 m for the pre-Libby Dam era 

(n = 599) and 147 m (n = 145) for the Libby Dam era. The 

following analysis is based on the channel-geometry profiles 

for 20 stream-gaging measurements made from 1931 to 

1970 and for 20 stream-gaging measurements made from 

1978 to 1993 (fig. 16). Each channel-geometry profile is 

based on about 40 depth measurements that were made 

during the measurement of streamflow discharge. During 

the period of record, the river channel migrated toward the 

northeast and toward the southwest on somewhat of a 

cyclical basis. During the pre-Libby Dam era and the Libby 

Dam era, the right bank migrated over a distance of about 7 

m and 15 m and the left bank migrated about 11 m and 20 

m, respectively. The distance the channel migrates laterally 

varies with time and represents less than 14 percent of the 

overall width of the channel.

AGGRADATION AND DEGRADATION OF 

RIVERBED

The most notable change during the Libby Dam era 

was the initiation of cyclical aggradation and degradation of 

the riverbed in the center of the channel at the Copeland 

cableway. After the closure of Libby Dam, the riverbed 

beneath the Copeland cableway aggraded by about 0.5 to 

1.0 m between the left bank and center and remained unchanged near the right bank (fig. 16). The aggradation and 

degradation are reflected in a twofold increase in the fluctuation of the minimum riverbed elevation measured beneath 

the Copeland cableway during regular flow measurements 

(fig. 17). The minimum riverbed elevation between 1931 

and closure of Libby Dam ranged from 522.6 to 521.3 m 

(n = 599), a fluctuation of 1.3 m, and during the Libby Dam 

era, ranged from 522.4 to 519.9 m (n = 145), a fluctuation of 

2.5 m. Dune movement is a likely explanation for some of 

the fluctuation in riverbed elevation. Closure of Libby Dam 

did not influence the long-term mean elevation of the riverbed beneath the Copeland cableway (fig. 18): 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.

Composition of Channel Substrate

Seismic subbottom profiling and sediment coring 

provided the basic data for characterizing the composition 

of substrate in the Kootenai River white sturgeon spawning 

reach. Cross sections of the Kootenai River at 19 locations 

show channel geometry, seismic subbottom profile, sediment core(s), and the substrate sediment texture (fig. 23). 

The depth of subsurface exploration is generally sufficient 

for describing the alluvial sediment deposited prior to and 

since the closure of Libby Dam in the Kootenai River where 

white sturgeon currently spawn. The basis for this assessment is provided in the following paragraphs.

Although the bottom of this river is covered mainly 

with alluvial sediment, a regional lacustrine clay-silt layer 

underlies and, to a limited extent, forms the bottom of the 

Kootenai River throughout most of the spawning habitat, as 

can be seen in sediment cores along a longitudinal section of 

the river between RKM 239.7 and 225.8 (fig. 19C) and in 

some seismic subbottom profiles (fig. 23H). The contact 

between the alluvial sand and the underlying dense clay-silt 

layer indicates the minimum possible riverbed elevation 

since the closure of Libby Dam. Clay-silt layers are deposited only at low velocities. For example, Hjulstrom (1935, 

p. 298) found that the silts and clays he studied settled at 

flow velocities of less than 0.01 m/s. Such stagnant 

streamflow conditions have not existed during the period of 

record at the Copeland gage (1929–93). Alluvial sediment 

lying above the lacustrine layer includes any sediment 

deposited since the retreat of glacial Kootenay Lake. 

Geologist striplogs for sediment cores along a longitudinal section of the river from RKM 241.6 to 229.5 show 

the contact between alluvial sediments and lacustrine clay in 

the spawning reach (fig. 19B). In these cores, the depth 

below the river channel to the first dense clay-silt layer 

ranged from 0.2 m in core K14-TH to 1.6 m in core K5-C.

The contact between alluvial deposits for the preLibby Dam and the Libby Dam eras could not be identified. 

However, inferences about alluvial sediment deposition and 

scouring since the closure of Libby Dam were made on the 

basis of (1) changes in the particle size of sediment with 

depth below the riverbed, and (2) the maximum probable 

aggradation of the channel substrate during the Libby Dam 

era. A 2.5-m fluctuation of the minimum riverbed elevation 

was measured in the thalweg beneath the Copeland cableway during the Libby Dam era (fig. 18). This fluctuation 

indicates that during the Libby Dam era, the channel substrate aggraded by 2.5 m and also degraded by nearly the 

same amount. 

A 2.5-m depth criterion was selected to establish a 

maximum depth for the contact between sediments deposited on the riverbed during the Libby Dam era and the 

underlying sediments deposited prior to the closure of Libby 

Changes in Channel Geometry and Substrate 17
Dam. A caveat applies to this depth criterion: channelgeometry data at the Copeland gaging station indicate that 

the channel substrate in parts of the meander reach may not 

have undergone aggradation, may have remained relatively 

stable, or may have undergone degradation. 

Inferences about alluvial sediment deposition and 

scouring since the closure of Libby Dam are: (1) where a 

sediment core penetrated a sand layer less than 2.5 m thick 

that overlies a lacustrine clay-silt layer, it is assumed that 

gravel and cobble were not present above the lacustrine 

layer at the time of the closure of Libby Dam; (2) where a 

sediment core penetrated only alluvial sand and organic 

matter to a depth greater than 2.5 m, it is assumed that a 

gravel and cobble layer was not present on the riverbed at 

the time of the closure of Libby Dam; and (3) where a sediment core penetrated a layer of sand less than 2.5 m thick, 

then a gravel layer and a lacustrine clay-silt layer, it is 

assumed that the gravel layer existed prior to the closure of 

Libby Dam and subsequently was buried.

GENERAL DESCRIPTION OF SUBSTRATE

Alluvial sand forms active sand dunes in the Kootenai 

River throughout all but the uppermost reach of the white 

sturgeon spawning habitat. The vertical relief of these dunes 

varies from less than 0.3 m to more than 2 m, and most are 

less than 1.3 m. On the basis of the geologist logs for the 

sediment cores (fig. 24), the mineralogical composition of 

the alluvial sand varies widely, ranging from granitic to 

metamorphic mineral assemblages with an overall abundance of quartz, feldspar, biotite, and mica. Sand color 

ranges predominantly from light to medium olive gray, with 

isolated occurrences of dark yellowish brown. Alluvial 

sand-grain diameters range from very fine (0.125 mm) to 

very coarse (2.0 mm) with a predominance of mediumgrained sand (0.5–1.0 mm). Ponar dredge samples of the 

riverbed (table 2) show fine- to coarse-grained alluvial sand 

at the 22 locations sampled between RKM 226 and 244.3. 

Sand-grain diameters tend to decrease along the inside bend 

of meanders. The sand tends to be moderately sorted to well 

sorted and individual grains are subrounded to subangular. 

The sand layer contains traces of shell fragments such as 

those identified at 1.9 m below the riverbed in sediment core 

K3-C (fig. 24A), taken near the center of cross-section S-S' 

(fig. 2C).

The alluvial sand generally included layers of 

organic-rich debris composed mainly of wood fragments. 

The thickness of some organic-rich layers was slightly 

greater than 0.2 m, such as the case in sediment core K11-

LB (fig. 20 and fig. 24S). These layers typically appeared as 

thin black lamina less than 3 cm thick. Some of the wood 

fragments are charred, evidence that the material originated 

in a forest fire. The sediment cores essentially show that 

thin, discontinuous layers of organic debris are ubiquitous in 

the sandy layer. Organic debris sometimes covers the river 

floor in the deepest part of the thalweg.

Gravel and cobble are exposed along the bottom of 

the Kootenai River in the braided reach and are exposed 

intermittently in the upstream part of the buried gravelcobble reach. Sediment cores of alluvial sand overlying 

gravel and cobble layer(s) have been divided into two populations on the basis of depth. Cores K9.5-C, K9.5-TH, 

K15.5-TH, K18-TH, and K20-TH (fig. 24L, fig. 24M, 

fig. 24CC, fig. 24HH, and fig. 24II) have less than 1 m of 

sand overlying a gravel and cobble layer. Cores K10-TH2, 

K12-TH1, and K12-TH2 (fig. 24Q, fig. 24V, and fig. 24W) 

have 1 to 2.9 m of sand overlying a cobble and gravel layer.

The lacustrine clay-silt layer is generally dense, dry, 

and stiff, ranges from light to dark olive gray, and is mottled 

in some samples. This layer contains layers of silt and very 

fine sand and a few thin lenses of shell fragments. The riverbanks below the natural levee and the dike typically are incised into the regional lacustrine clay-silt layer. Some of the 

riprap and sediment added to the levee and dike have 

slumped onto the submerged riverbank and have covered 

the lacustrine clay-silt layer. 

BRAIDED REACH

Cobble and gravel-bar substrate occurs throughout the 

braided reach (fig. 21A) and forms multiple channels at low 

flow. The gravel bars extend some distance downstream 

from U.S. 95 Bridge, roughly 0.5 RKM. The Idaho Department of Transportation (IDOT) made several test borings in 

the river at the bridge. The IDOT geologist log for test 

boring DH-7 in the center of the channel at the bridge 

(fig. 19A) shows that gravel deposits extend at least 30 m 

below the river. This test boring did not penetrate the 

regional lacustrine layer. On the basis of this log and of 

seismic subbottom profiles at cross sections A-A' and B-B' 

(fig. 2A, fig. 23A, and fig. 23B), the regional lacustrine 

clay-silt layer is completely or severely eroded beneath the 

river in the vicinity of the U.S. 95 Bridge.

The boundary between the braided reach and the 

buried gravel-cobble reach shifts upstream and downstream 

in response to changes in sediment transport. A high-flow 

event in 1996 during the Libby Dam era apparently caused a 

small but noticeable degradation of the sand layer, burying 

gravel and cobble near the downstream end of the braided 

reach. Patrick McGrain (Bureau of Reclamation, oral 

commun., 2000) observed muddy-silty-sandy sediment 

beneath part of the U.S. 95 Bridge during 1993 and 1994. 

After the large 1996 spring runoff event (USGS measured 

1,263 m3/s of streamflow from the U.S. 95 Bridge in 

Bonners Ferry on June 7, 1996), Pat McGrain observed that 

the river substrate beneath the bridge and for an undeter18 Suspended-Sediment Transport, Kootenai River, Idaho
mined distance downstream toward the railroad bridge at 

RKM 245.6 was covered with clean cobble. 

BURIED GRAVEL-COBBLE REACH

The streambed surface in the buried gravel-cobble 

reach, RKM 241.1 to 245.75, is predominantly alluvial sand 

deposited on a discontinuous gravel, cobble, and sand layer 

or deposited unconformably on the regional lacustrine claysilt layer (fig. 21A and fig. 21B). At the upstream end of this 

reach, the streambed consists of gravel, cobble, and sand. 

On the basis of limited data, the composition of the streambed alluvium in this reach is such that the percentage of 

cobble and gravel decreases and the percentage of sand increases in the downstream direction. Upstream from the 

sharp riverbend at RKM 244.5, where Ambush Rock is 

exposed along the southern bank of the river, the substrate is 

noticeably less sandy and contains greater amounts of gravel 

and cobble.

Seismic subbottom profiles and sediment cores 

collected in this reach show that a thin layer of sand overlies 

a discontinuous layer of cobbles, gravel, and sand. Sediment core K-18TH (fig. 22 and fig. 24HH), collected near 

the river’s right bank at cross-section E-E' (fig. 23E), penetrated a 0.7-m-thick layer of sand and organic debris; a 0.2-

m-thick layer of gravel, cobble, sand, and organic debris; a 

0.69-m-thick layer of sand and organic debris; and the upper 

0.7 m of the regional lacustrine clay-silt layer. Where the 

cobble, gravel, and sand layer is not present, alluvial sand 

overlies the lacustrine clay-silt layer. Sediment core 

K-18LB (fig. 24GG), on the opposite side of the river near 

the left bank, penetrated a 2.6-m-thick layer of sand and 

organic debris and the upper 0.9 m of the regional lacustrine 

clay-silt layer, but no gravel-cobble-sand layer. Farther 

upstream in this reach, sediment core K20-TH, at crosssection D-D' (fig. 23D and fig. 24II), penetrated a 0.9-mthick layer of sand and organic debris; a 0.2-m-thick layer of 

gravel, cobble, and sand; and 0.3 m of sand, whereupon the 

core barrel could not be advanced into the substrate (refusal 

depth). The refusal depth for coring represents a change in 

sediment texture, the base of a silty sand layer and top of 

another layer of gravel and cobble. Here, a seismic subbottom profile recorded a seismic reflector at about 5 m 

below the streambed that likely indicates the top of the 

regional lacustrine layer (fig. 23D). 

MEANDER REACH 

The channel substrate in the meander reach is a 

reflection of channel morphology. Straight reaches, such as 

near cross-sections J-J' and R-R' (fig. 2B, fig. 23J, and fig. 

23R), typically have flat bottoms composed of alluvial sand 

to a depth of at least 3.5 m below the streambed, the 

maximum depth that was cored. Seismic data indicate that 

the thickness of the alluvial sand generally ranges from 5 to 

10 m below the riverbed (fig. 23H). Meanders have 

pronounced thalwegs more than 9 m deep near the outside 

banks (fig. 23H, fig. 23I, fig. 23K, fig. 23L, and 

fig. 23P). Seismic and sediment core data indicate that 

meander thalwegs generally incised into the lacustrine claysilt layer; however, the lacustrine layer can be overlain with 

sand or organic debris. Other parts of the channel bed 

consist of alluvial sand deposited on the lacustrine clay-silt 

layer. Along inside banks, the alluvial sand deposited over 

the lacustrine clay-silt layer is locally thicker than the 3.5-m 

vibracore depth penetration. These sands have been shaped 

into dunes as high as 2 m. Sediment with a diameter greater 

than sand (granules, gravel, cobbles, and riprap) is present 

in the channel substrate in very small amounts downstream 

from Deep Creek near cross-sections G-G' and I-I' and 

downstream from Myrtle Creek in the general vicinity of 

cross-sections L-L' and K-K'. Gravel and cobble are not 

present in the most prolific white sturgeon spawning reach 

near Shorty Island. 

Upstream from Myrtle Creek

The substrate of the Kootenai River meander reach 

upstream from Myrtle Creek is predominantly sand and 

some lacustrine clay (fig. 19B). For example, on the steep 

face of the thalweg near the right bank at cross-section H-H' 

(fig. 2B and fig. 23H), sediment core K13-RB penetrated 

the regional lacustrine clay-silt layer. Here, sand covers the 

riverbed between the thalweg and the left bank, with thickness increasing toward the left bank. Cores K13-LB1 and 

K13-LB2 penetrated more than 2.5 m of alluvial sand 

(fig. 24X and fig. 24Y). Farther downstream near Myrtle 

Creek at cross-section J-J' (fig. 23J), sediment cores K11-

LB and K11-C penetrated more than 2.5 m of sand (fig. 24S

and fig. 24T). Where sediment cores penetrated only 

alluvial sand and organic matter to a depth of 2.5 m or 

greater, it is assumed that a layer of gravel or cobble was not 

present on the riverbed at the time of closure of Libby Dam. 

The river substrate prior to the closure of Libby Dam is 

similar to the present condition, lacking gravel and cobble 

spawning substrate needed for white sturgeon recruitment.

Two sediment cores of the Kootenai River substrate 

between the mouth of Deep Creek and the mouth of Myrtle 

Creek penetrated sediment with a particle size greater than 

sand. Near the left bank at RKM 238.9, upstream from 

cross- section G-G' (fig. 23G), sediment core K15.5-TH 

penetrated 0.02 m of wood debris, 0.4 m of granules (diameter 2–4 mm, between sand and gravel size), 1.6 m of 

sand, 0.05 m of lacustrine clay, and 1.5 m of sand 

(fig. 24CC). The granule layer is limited to the outside of 

this gentle riverbend where flow velocities are greatest. The 

source of the granules is likely a large runoff event in Deep 

Creek. Because these granules are on the riverbed surface, 

the runoff event most likely occurred during the Libby Dam 

Changes in Channel Geometry and Substrate 19
era. The clay-silt layer indicates the minimum possible 

riverbed elevation since the closure of Libby Dam; therefore, gravel or cobble substrate was not present at the coring 

site at the time of closure of Libby Dam (fig. 23G and 

fig. 24CC). Sediment core K12-TH1, near the thalweg at 

cross-section I-I', penetrated 3 m of sand and organic debris 

and 0.4 m of fine gravel (fig. 23I and fig. 24V). This layer 

of fine gravel was probably buried by sand prior to the 

closure of Libby Dam. 

Downstream from Myrtle Creek

There is evidence of gravel, cobble, and larger sediment buried by a thin layer of sand and lying exposed on the 

riverbed in the spawning reach below Myrtle Creek, between RKM 233.5 and 234.7 (fig. 21B). The source, as well 

as the extent, of the large-diameter sediment is unclear. 

Along part of this spawning reach, riprap on the dike left 

bank may have rolled into the channel. Here, sediment cores 

did not penetrate the regional lacustrine clay-silt layer.

Downstream from Myrtle Creek at cross-section 

K-K', between the thalweg and left bank (outside bend of 

the meander), gravel and larger sediment lie on the riverbed 

and are locally buried by thin layers of sand (fig. 23K). 

Here, a seismic subbottom profile shows several parabolic 

reflectors at or just below the riverbed in the thalweg and 

between the thalweg and left bank. These reflectors indicate 

the presence of cobble or riprap. Sediment core K10-TH1 

(fig. 24P), taken in the thalweg at cross-section K-K', 

penetrated a few centimeters of the riverbed and did not 

recover sediment; this core was assumed to have met with 

gravel, cobble, or riprap. Sediment core K10-TH2 

(fig. 24Q), also taken in the thalweg, penetrated about 0.7 m 

of sand and then 0.1 m farther into a layer of gravel, and 

could not be advanced farther into the riverbed. Sediment 

cores K10-RC and K10-RTH (fig. 24O and fig. 24R), 

located between the thalweg and right bank in the 

depositional side of the meander, penetrated 3.5 m and 2.1 

m of sand and organic debris, respectively.

Downstream from Myrtle Creek, in the thalweg at 

cross-section L-L', sediment core K9.5-TH penetrated 0.2 m 

of sand and then struck gravel, cobbles, or riprap that prevented the core from advancing farther into the riverbed; 

there was no recovery of sediment (fig. 23L and fig. 24M). 

Sediment core K9.5-C (fig. 24L), taken in the center of the 

river, penetrated about 2.1 m of sand and could not be advanced farther into the riverbed. The bottom of the core 

barrel had numerous pea-gravel-size indentations, indicating 

the presence of gravel; however, gravel was not recovered 

in the core barrel. Sediment core K9.5-RB (fig. 24N), taken 

between the right bank and center of the river, penetrated 

3.5 m of sand and organic fragments. 

The Kootenai River meander below Myrtle Creek and 

near the base of Cascade Ridge appears to have incised into 

an alluvial fan composed of gravel, cobble, and sand 

(fig. 21B). The meander bend is within 183 m of the base of 

Cascade Ridge. The 1983 Kootenai Flats erosion shift maps 

(U.S. Army Corps of Engineers, 1983) show that Lost 

Creek, Cascade Creek, and Myrtle Creek incise into 

alluvial-fan deposits. The alluvial-fan deposits are composed of sand, gravel, and cobble. The channel geometry at 

cross-section K-K' appears to support the presence of an 

alluvial fan at this section (fig. 23K). Here, the channel 

geometry is significantly different from that of other cross 

sections. The submerged left bank that forms the face of the 

thalweg along the outside riverbend is much more gently 

inclined than elsewhere in the meander reach of the white 

sturgeon spawning habitat. The relatively gentle sloping 

face of the thalweg includes a collapse feature along the 

riverbed below depths of about 4 m. This collapse feature 

suggests that the face of the thalweg along the left bank is 

not composed of a stiff, cohesive, lacustrine clay-silt layer 

and silt that can support a steep thalweg but is instead 

composed of noncohesive silt, sand, gravel, and cobble that 

tend to lack the intrinsic properties needed to support a steep 

thalweg face. 

The Kootenai River at cross-section M-M' (fig. 23M), 

located at the downstream end of the white sturgeon spawning reach below Myrtle Creek, is dominated by sand across 

the river: sediment cores K9-LB, K9-C, and K9-RB penetrated only sand (fig. 24I, fig. 24J, and fig. 24K). The seismic subbottom profile of cross-section M-M' shows sand 

filling in the thalweg near the left bank. The seismic subbottom profile near the left bank shows a seismic reflector at 

11 m below the riverbed. The capacity of the seismic sound 

wave to propagate and reflect off a layer at a depth of 11 m 

indicates that a layer of gravel and cobble is not present in 

the substrate to a depth of 11 m.

Shorty Island

Sediment cores and seismic subbottom profiles 

obtained in the Kootenai River white sturgeon spawning 

reaches near Shorty Island—RKM 230.0–231.0 and 228.7–

229.5—show that the substrate composition is similar to that 

which existed before closure of Libby Dam. There is no 

indication of gravel or cobble in the substrate near Shorty 

Island (fig. 21C).

In this reach, seismic subbottom profiles and sediment 

cores were obtained at cross-sections P-P' and Q-Q'. Crosssection P-P' shows that the riverbed forms a sloping terrace 

between the center and the right bank (fig. 23P). Near the 

left bank, sediment core K6-LB penetrated 3.5 m of sand 

(fig. 24E). It is assumed that at this location a layer of 

gravel or cobble was not present on the riverbed at the time 

of closure of Libby Dam. The thalweg, between the right 

bank and center of the channel, is incised into the regional 

lacustrine clay-silt layer. The lower part of the thalweg is 

20 Suspended-Sediment Transport, Kootenai River, Idaho
covered with a veneer of sand. At cross-section Q-Q', the 

thalweg is located along the right bank and incised into the 

lacustrine clay-silt layer, which is exposed at the bottom of 

the thalweg (fig. 23Q). Sediment core K5-C (fig. 24D) and 

the seismic subbottom profile at cross-section P-P' show that 

sand is present on the riverbed and the thickness of the sand 

increases from the thalweg toward the left bank. Sediment 

core K5-C penetrated 1.6 m of sand and 1.6 m of lacustrine 

clay and silt. It is assumed that at this location a layer of 

gravel or cobble was not present on the riverbed at the time 

of closure of Libby Dam.

EFFECTS OF CHANGES IN SUSPENDEDSEDIMENT TRANSPORT AND CHANNEL 

SUBSTRATE ON WHITE STURGEON 

SPAWNING SUBSTRATE

The white sturgeon spawning substrate in the 

Kootenai River has been affected in some areas by changes 

in suspended-sediment transport and channel substrate. 

Assessment of the effects is based, in part, on suspendedsediment samples and stream-gaging measurements from 

the Copeland gage, located 15 RKM below the spawning 

habitat, for the period of record 1929–93. As previously 

discussed, data collected from the Copeland gage appear to 

be a reasonable surrogate for describing changes in the 

white sturgeon spawning reach because both the gage and 

nearly all of the spawning reach are located in backwater. 

The degree to which the fluctuation of channel substrate at 

Copeland could be compared with that in the spawning 

reach could not be determined.

After the closure of Libby Dam in 1972, the Kootenai 

River transported smaller volumes of suspended sand 

through the white sturgeon spawning reach that lies within 

the buried gravel-cobble reach and meander reach. During 

the Libby Dam era, the annual suspended-sediment load 

leaving the Kootenai River white sturgeon spawning reach 

decreased about sixfold (fig. 9C). On the basis of a small set 

of suspended-sediment samples, the river appears to be 

transporting finer grained sediment in suspension since the 

closure of Libby Dam. The percentage of sand-size particles 

in suspended-sediment samples collected during spring and 

early summer high flows at the Copeland gage is less than in 

samples collected during the pre-Libby Dam era (fig. 15). 

The reduction in peak flows during the Libby Dam era has 

reduced the Kootenai River’s capacity to transport suspended sediment through the spawning reach. The reduction 

in peak flow has also resulted in a larger proportion of finer 

grained sediment in suspension. Contributing to the decrease in suspended-sediment load in the spawning reach is 

the loss of 70 percent of the basin after the closure of Libby 

Dam. Monitoring the sediment load transported into and out 

of the spawning reach over a period of several years could 

address whether or not sand is accumulating in the spawning 

reach, but this is a resource-intensive investigation 

(Andrews, 1984).

Since the closure of Libby Dam, the most notable 

change in channel geometry beneath the Copeland streamgaging cableway was the initiation of cyclical degradation 

and aggradation of the riverbed in the center of the channel, 

which is reflected in a twofold increase, from 1.3 to 2.5 m, 

in the fluctuation of the minimum riverbed elevation beneath the cableway (fig. 17). The fluctuation of minimum 

riverbed elevation suggests that during the Libby Dam era, 

parts of the riverbed in the spawning reach may have aggraded or degraded by as much as 2.5 m. The change in the 

minimum riverbed elevation at Copeland during the Libby 

Dam era is considered a reasonable estimate of the maximum thickness of alluvial sediment possibly deposited on 

the Kootenai River white sturgeon spawning reach since the 

closure of Libby Dam. This information helped determine 

that the depth of seismic exploration and sediment coring, 

which on average exceeded 2.5 m, was sufficient to sample 

and describe any alluvial sediment that formed the riverbed 

just prior to the closure of Libby Dam and that was subsequently buried by alluvial sediment after the closure of 

Libby Dam. 

The sediment texture of channel substrate in the 

buried gravel-cobble reach, RKM 241.1 to 245.75, within 

the white sturgeon spawning reach indicates sand accumulation during the Libby Dam era. This cyclical process of 

degradation and aggradation of the riverbed sediment is the 

most likely cause of alternating gravel-cobble layers and 

sand layers in sediment core K18-TH in the reach 

(fig. 24HH). Gravel and cobble layers in this core are 

present at 0.7 to 0.9 m and 1.4 to 1.5 m below the riverbed. 

In the buried gravel-cobble reach, there was a greater 

propensity for aggradation and degradation of sand over the 

discontinuous gravel and cobble layers before the closure of 

Libby Dam than after. Unregulated spring snowmelt-runoff 

flows flushed part of the sand layer and exposed some of the 

buried gravel-cobble layer because streamflow velocities 

were higher. The transport of gravel and cobble into this 

reach was much greater before the closure of Libby Dam 

than after. One source of this gravel and cobble is located a 

short distance upstream at the U.S. 95 Bridge near Bonners 

Ferry. Here, the center of the channel contains a large volume of gravel and cobble at least 30 m thick, as shown in 

sediment core DH-7 (fig. 19A). In this reach where the river 

is under backwater conditions, unregulated fall-winter base 

flows gradually deposited silt and sand and reestablished a 

sand layer, burying the gravel-cobble layer. 

Effects of Changes in Suspended-Sediment Transport and 

Channel Substrate on White Sturgeon Spawning Substrate 21
White sturgeon spawning substrate in the meander 

reach is currently composed of alluvial sand that forms sand 

dunes and of minor amounts of lacustrine clay and silt generally found in the rivers thalweg. The data presented in this 

report show that the present substrate composition in the 

meander reach is considered similar to that which existed 

prior to closure of Libby Dam, with one possible exception. 

Prior to the closure of Libby Dam, minor amounts of gravel 

and cobble may have been exposed on the riverbed in the 

spawning reaches just below the mouth of Myrtle Creek 

near cross-sections L-L' and K-K'. 

Seismic subbottom profiles and coring in the white 

sturgeon spawning reach below Myrtle Creek, between 

RKM 233.5 and 234.7 (fig. 2B) in the vicinity of K-K' and 

L-L' (fig. 23K and fig. 23L), provided evidence of gravel, 

cobble, and larger sediment buried by a thin layer of sand or 

lying exposed on the riverbed. The source, as well as the 

extent, of the large-diameter sediment is subject to speculation. Along part of this spawning reach, riprap on the dike 

left bank may have rolled into the channel. The thalweg 

along the outside bend of the meander could be incised into 

an alluvial fan (composed of a mixture of gravel, cobble, 

and sand) that extends from Cascade Ridge. During the preLibby Dam era, the higher spring-summer flows may have 

scoured the sand, exposing this gravel and cobble. 

Sediment cores and seismic subbottom profiles 

obtained in the most active Kootenai River white sturgeon 

spawning reach, near Shorty Island, show that the current 

substrate composition is similar to that which existed prior 

to closure of Libby Dam. There is no indication of gravel or 

cobble in the substrate near Shorty Island (fig. 21C).

SUMMARY AND CONCLUSIONS

A year-long field study was conducted in cooperation 

with the Kootenai Tribe of Idaho along a 21.7-kilometer 

reach of the Kootenai River including the white sturgeon 

spawning reach near Bonners Ferry, Idaho, which is located 

111 kilometers downstream from Libby Dam. Temporal 

changes in the daily and annual suspended-sediment loads 

leaving the white sturgeon spawning reach were characterized during 1966–83 using historical data collected at the 

U.S. Geological Survey streamflow-gaging station at Copeland, Idaho. In addition, temporal changes in suspendedsediment loads were characterized at a U.S. Geological 

Survey stream-gaging station in Libby, Montana, for a brief 

period prior to and after the closure of Libby Dam. Changes 

in channel geometry were evaluated at the Copeland gage, 

located 159 kilometers downstream from Libby Dam for the 

period of record, 1929–93. The gage was deactivated in 

1994. During the time of this study, there were no streamflow gages in the white sturgeon spawning reach located 

111 to 129 kilometers below Libby Dam. The Copeland 

stream-gaging data are used as a surrogate to describe 

changes in suspended-sediment transport and channel 

geometry in the spawning reach because of similar conditions at the Copeland gage and the spawning reach: both are 

located in the meander reach and in backwater. 

During the field study, data were collected in order to 

map the channel substrate in the white sturgeon spawning 

reach. These data include seismic subbottom profiles at 18 

cross sections of the river and sediment cores taken at or 

near the seismic cross sections. Generally, one core was 

taken from the deepest part of the thalweg where erosion 

may occur and another in shallower water where deposition 

may occur. Thirty cores were collected using a vibracoring 

system and five cores were collected using a piston coring 

system. The vibracoring system is equipped with a 0.08-

meter-diameter core barrel that is 3.66 meters in length and 

capable of recovering the clay-silt layer, silt, sand, gravel, 

and some cobble. Twenty-two vibracores sampled 3 to 3.5 

meters of the channel substrate. The piston coring system is 

equipped with a 0.08-meter-diameter core barrel that is 1.52 

meters in length. The maximum recovery for the piston core 

was 0.8 meter and the average recovery was 0.6 meter. Because of the limited resolution of seismic subbottom profiles 

and a limited number and distribution of sediment cores, the 

contact lines defining the composition of the river substrate 

are general delineations and inferred in most cases.

The annual suspended-sediment load leaving the 

Kootenai River white sturgeon spawning reach decreased 

dramatically after the closure of Libby Dam in 1972: mean 

annual pre-Libby Dam load during 1966–71 was 1,743,900 

metric tons, and the dam-era load during 1973–83 was 

287,500 metric tons. The lower peak flows during the Libby 

Dam era have reduced the Kootenai River’s capacity to 

transport suspended sand through the white sturgeon 

spawning reach. The amount of sand-size particles in suspended-sediment samples collected at Copeland during 

spring and early summer high flows after the closure of 

Libby Dam is roughly 50 to 75 percent less than in samples 

collected during the pre-Libby Dam era. Under these conditions, sand and silt may accumulate at a faster rate in the 

white sturgeon spawning reach than during the Libby Dam 

era. However, the supply of sand to the spawning reach is 

currently less as a result of the reduction of high flows and a 

loss of 70 percent of the basin after the closure of Libby 

Dam. The river’s reduced capacity to transport sand out of 

the spawning reach is compensated to an unknown extent by 

a reduced load of sand entering the spawning reach. There is 

insufficient suspended-sediment data to determine whether 

sand is accumulating in the spawning reach within the 

meander reach; however, sediment cores indicate sand 

accumulation in the buried gravel-cobble reach. 

22 Suspended-Sediment Transport, Kootenai River, Idaho
Since the closure of Libby Dam, the most notable 

change in channel geometry beneath the Copeland streamgaging cableway was the initiation of cyclical aggradation 

and degradation of the sand riverbed in the center of the 

channel. Aggradation and degradation of the riverbed are 

reflected in a twofold increase, from 1.3 to 2.5 meters, in the 

fluctuation of the minimum riverbed elevation beneath the 

Copeland cableway for the period of record 1929–71 and 

1973–93. This maximum fluctuation of the minimum riverbed elevation suggests that during the Libby Dam era, parts 

of the riverbed in the spawning reach may have aggraded or 

degraded by as much as 2.5 meters. The maximum fluctuation of the minimum riverbed elevation at Copeland 

during the Libby Dam era is considered a reasonable estimate of the maximum thickness of alluvial sediment 

possibly deposited on the Kootenai River white sturgeon 

spawning reach since the closure of Libby Dam. This 

information helped determine that the depth of seismic exploration and sediment coring, which on average exceeded 

2.5 meters, was sufficient to sample and describe any 

alluvial sediment that formed the riverbed just prior to the 

closure of Libby Dam and that was subsequently buried by 

alluvial sand and silt after the closure of Libby Dam. 

The white sturgeon spawning substrate in the 

Kootenai River has been affected in some areas by changes 

in suspended-sediment transport and channel substrate after 

the closure of Libby Dam. Before the closure of Libby Dam, 

there was probably a greater propensity for aggradation and 

degradation of sand over the discontinuous gravel and 

cobble layers in the buried gravel-cobble reach at Bonners 

Ferry. Unregulated high-velocity spring snowmelt-runoff 

streamflows flushed part of the sand layer and exposed 

some of the buried gravel-cobble layer. Unregulated fallwinter base flows gradually deposited silt and sand and 

reestablished a sand layer, burying the gravel-cobble layer. 

This cyclical process of aggradation and degradation of the 

riverbed sediment is reflected in the alternating gravelcobble layers and sand layers found in sediment core 

K18-TH. White sturgeon spawning substrate in the 

Kootenai River meander reach is currently composed of 

alluvial sand that forms sand dunes and of minor amounts of 

lacustrine clay and silt that are generally found in the river’s 

thalweg. The present substrate composition in the meander 

reach is considered similar to that which existed prior to 

closure of Libby Dam, with one possible exception. Prior to 

the closure of Libby Dam, minor amounts of gravel and 

cobble may have been exposed on the riverbed in the 

spawning reach just below the mouth of Myrtle Creek. The 

substrate composition near Shorty Island, a notable white 

sturgeon spawning reach, is predominantly sand and is 

similar to that which existed prior to closure of Libby Dam. 

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in the Columbia River downstream from McNary 

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v. 122, p. 217–227.

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enhancement of fisheries management: Stream 

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report 151: Olympia, Wash., Washington Department 

of Fisheries, 28 p.

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(Acipenser transmontanus): Portland, Oreg., variously 

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24 Suspended-Sediment Transport, Kootenai River, Idaho
Manuscript approved for publication, February 4, 2004

Prepared by U.S. Geological Survey Publishing staff

Washington Water Science Center, Tacoma, Washington:

Bob Crist

Bill Gibbs

Linda Rogers

Judith A. Wayenberg

Idaho District, Boise, Idaho:

Linda Buckmaster

Linda K. Channel

Richard Helton

For more information concerning the research in this report, contact the

Washington Water Science Center Director

U.S. Geological Survey, 1201 Pacific Avenue—Suite 600

Tacoma, Washington 98402 

http://wa.water.usgs.gov
Barton, Gary J .— Characterization of Channel Substrate, and Changes in Suspended-Sediment Transport and Channel Geometry in White 

Sturgeon Spawning Habitat in the Kootenai River near Bonners Ferry, Idaho, Following the Closure of Libby Dam — WRIR 03–4324