Prepared in cooperation with the Kootenai Tribe of Idaho

Bathymetric Surveys of the Kootenai River near Bonners Ferry, 

Idaho—Water Year 2011

U.S. Department of the Interior

U.S. Geological Survey

Data Series 694
Front cover: Ambush Rock (foreground) and Clifty Mountain (background) photographed from the Kootenai River, 

Idaho. Photograph taken June 2011 by Ryan L. Fosness, U.S. Geological Survey.

Back cover: Tree root wads used to protect the levees along the Kootenai River near River Mile 134, Idaho.

Photograph taken June 2011 by Ryan L. Fosness, U.S. Geological Survey.
Bathymetric Surveys of the Kootenai River near 

Bonners Ferry, Idaho—Water Year 2011

By Ryan L. Fosness

Prepared in cooperation with the Kootenai Tribe of Idaho

Data Series 694

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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Suggested citation:

Fosness, R.L., 2013, Bathymetric surveys of the Kootenai River near Bonners Ferry, Idaho, water year 2011: 

U.S. Geological Survey Data Series 694, 26 p.
iii

Contents

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

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

Description of Study Area ...................................................................................................................2

Bathymetric Data Collection Areas for Water Year 2011 ...............................................................2

Methods...........................................................................................................................................................9

Quality Assurance and Quality Control ............................................................................................9

Quality Assurance........................................................................................................................9

Quality Control............................................................................................................................16

Bathymetric Survey Data ...........................................................................................................................18

Multibeam Echosounding Survey in Meander Reach..................................................................18

Substrate Enhancement Project near Shorty’s Island and Myrtle Creek..................................22

Braided Reach Cross-Section Monitoring Surveys......................................................................23

Acknowledgments.......................................................................................................................................24

References Cited..........................................................................................................................................24

Appendixes ...................................................................................................................................................25

Appendix A. Daily Logs ......................................................................................................................25

Appendix B. Quality Control Parameters Defined for Estimating Total 

Propagated Uncertainty.......................................................................................................25

Appendix C. Multibeam Echosounder Physical Offsets...............................................................25

Appendix D. Patch Test, April 28, 2011 ............................................................................................25

Appendix E. Patch Test, June 15, 2011 ............................................................................................25

Appendix F. Performance Test, April 28, 2011.................................................................................25
iv

Figures

1. Map showing location of study area in the Kootenai River drainage basin,

northern Idaho .............................................................................. 3

2. Map showing location of the Kootenai River white sturgeon critical habitat in

the study reach, near Bonners Ferry, Idaho ............................................. 4

3. Maps showing extent of the surveys in unmapped portions of the meander

reach, near Bonners Ferry, Idaho, water year 2011 .................................... 5

4. Map showing extent of the Shorty’s Island and Myrtle Creek substrate

enhancement study area, near Bonners Ferry, Idaho, water year 2011 ............ 7

5. Map showing extent of the braided reach cross-section survey area, near

Bonners Ferry, Idaho, water year 2011 ................................................... 8

6. Example of the angular coverage and number of beams for the multibeam

echosounder ................................................................................. 10

7. Photograph showing multibeam echosounder components and mount on

USGS research vessel ..................................................................... 11

8. Photograph showing close-up view of the submerged components of the

multibeam echosounder .................................................................. 12

9. Photograph showing data acquisition, processing, and display components

for the MBE system ........................................................................ 13

10. Patch test lines and resulting bathymetry from Lake Coeur d’Alene near

Cougar Bay, Idaho........................................................................... 15

11. Performance Test reference lines, standard lines, and resulting bathymetry

from Lake Coeur d’Alene near Cougar Bay, Idaho....................................... 17

Tables

1. Project quality assurance and quality control elements for multibeam

bathymetric surveys ........................................................................ 14

2. Quality-control results ..................................................................... 16

3. Multibeam echosounder bathymetric survey in meander reach ..................... 18

4. Substrate enhancement project near Shorty’s Island and Myrtle Creek ............ 22

5. Braided reach cross-section monitoring surveys ....................................... 23

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)
Bathymetric Surveys of the Kootenai River near 

Bonners Ferry, Idaho—Water Year 2011

By Ryan L. Fosness

Abstract

In 2009, the Kootenai Tribe of Idaho released and 

implemented the Kootenai River Habitat Restoration Master 

Plan. This plan aimed to restore, enhance, and maintain 

the Kootenai River habitat and landscape to support and 

sustain habitat conditions for aquatic species and animal 

populations. In support of these restoration efforts, the U.S. 

Geological Survey, in cooperation with the Kootenai Tribe 

of Idaho, conducted high-resolution multibeam echosounder 

bathymetric surveys in May, June, and July 2011, as a baseline 

bathymetric monitoring survey on the Kootenai River near 

Bonners Ferry, Idaho. Three channel patterns or reaches exist 

in the study area—braided, meander, and a transitional zone 

connecting the braided and meander reaches. Bathymetric 

data were collected at three study areas in 2011 to provide: 

(1) surveys in unmapped portions of the meander reach; 

(2) monitoring of the presence and extent of sand along 

planned lines within a section of the meander reach; and 

(3) monitoring aggradation and degradation of the channel 

bed at specific cross sections within the braided reach and 

transitional zone. The bathymetric data will be used to update 

and verify flow models, calibrate and verify sediment transport 

modeling efforts, and aid in the biological assessment in 

support of the Kootenai River Habitat Restoration Master 

Plan. The data and planned lines for each study reach 

were produced in ASCII XYZ format supported by most 

geospatial software.

Introduction

Anthropogenic influence to the Kootenai River (or 

Kootenay for the Canadian areas) is evident upstream 

of, within, and downstream of the federally designated 

critical-habitat reach of the Kootenai River population of 

white sturgeon (Acipenser transmontanus). The Kootenai 

River white sturgeon critical habitat is a 18 mi long reach 

extending from river mile (RM) 159.7, downstream of the 

Moyie River, to RM 141.7 in the meander reach downstream 

of Shorty’s Island (Federal Register, 2008).

Historical references indicate that dikes were built on 

natural levees early in the 20th century to protect agricultural 

areas in the Kootenai River floodplain from flooding 

(Turney-High, 1969; Boundary County Historical Society, 

1987; Redwing Naturalists, 1996). Changes to the natural 

river environment have led to detrimental conditions in the 

critical habitat reach. Additionally, the construction and 

operation of Libby Dam, put into service in 1972, substantially 

altered Kootenai River streamflow and water quality, and 

created a habitat unsuitable to sustain natural recruitment of 

the Kootenai River white sturgeon (U.S. Fish and Wildlife 

Service, 2006). Research by the Idaho Department of Fish and 

Game on sturgeon populations determined that there was a 

lack of juvenile sturgeon in all but four 1-year classes during a 

16-year period (Partridge, 1983).

In 1994, the U.S. Fish and Wildlife Service (USFWS) 

listed the Kootenai River population of white sturgeon as an 

endangered species under the provisions of the Endangered 

Species Act of 1973, as amended. The population was listed 

as endangered because of decreasing numbers and a lack of 

juvenile recruitment that was first noted in the mid-1960s 

(Federal Register, 1994; U.S. Fish and Wildlife Service, 

1999). Many researchers attributed these decreasing numbers 

and lack of recruitment to the degradation of white sturgeon 

habitat, particularly the habitat used for spawning (Paragamian 

and others, 2001, 2002; Kock and others, 2006). 

In 2006, the USFWS published a biological opinion that 

proposed habitat improvements designed to meet the criteria 

outlined in the Kootenai River white sturgeon recovery 

plan (U.S. Fish and Wildlife Service, 2006). One proposed 

improvement was, “a flow regime that limits sediment 

deposition and maintains appropriate rocky substrate for 

sturgeon egg adhesion, incubation, escape cover, and free 

embryo development...” (Federal Register, 2008, p. 39,513 

and 39,522).
2 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

In 2009, the Kootenai Tribe of Idaho released and 

implemented the Kootenai River Habitat Restoration Master 

Plan (hereinafter referred to as the “Master Plan”). The goal 

of the Master Plan is to restore, enhance, and maintain the 

Kootenai River habitat and landscape so that it supports and 

sustains habitat conditions for aquatic species and animal 

populations (Kootenai Tribe of Idaho, 2009). In support of 

these restoration efforts, the U.S. Geological Survey (USGS), 

in cooperation with the Kootenai Tribe of Idaho conducted 

bathymetric surveys of the Kootenai River during May, June, 

and July 2011, as a baseline monitoring survey within the 

braided and meander reaches of the Kootenai River near 

Bonners Ferry, Idaho. Bathymetric surveys on the Kootenai 

River provide: (1) surveys of unmapped portions of the 

meander reach; (2) surveys in the areas near Shorty’s Island 

and Myrtle Creek to support efforts for a potential substrate 

enhancement project; and (3) surveys within the braided reach 

at selected monitoring cross sections. Each of the surveys 

support short- and long-term adaptive management and 

monitoring as part of the Master Plan.

 This document presents the bathymetric data from 

each of the three surveys on the Kootenai River for water 

year 2011. A description of the study areas, data-collection 

methods, and quality-control and quality-assurance procedures 

are discussed to describe the data-collection efforts.

Description of Study Area

The Kootenai River is the second largest contributor to 

the Columbia River in terms of discharge volume (fig. 1). 

From its headwaters in the Rocky, Salish, and Purcell 

Mountains, the Kootenai River flows to the south through 

northwestern Montana. Turning west until reaching the base 

of the Cabinet Mountains, the river then flows north through 

the Kootenai Valley of northern Idaho. From there, the river 

reaches its terminus at Kootenay Lake in British Columbia, 

Canada, at the base of the Selkirk Mountains. In 1972, the 

U.S. Army Corps of Engineers managed the construction of 

Libby Dam on the upper Kootenai River near Libby, Montana, 

creating Lake Koocanusa. 

The study area described in this report lies within 

those parts of the Kootenai River within the State of Idaho 

(fig. 2) including the critical habitat. Three distinct channel 

patterns (hereinafter referred to as “reaches”) are in the study 

area: (1) A braided channel, consisting primarily of a gravel 

and cobble substrate, extending from RM 159.7 near the 

confluence of the Moyie River downstream to RM 152.9 near 

Bonners Ferry; (2) a meandering channel, primarily consisting 

of sand and lacustrine clay, extending from RM 152.9 

downstream approximately 78 mi to the confluence of the 

Kootenai River with Kootenay Lake in British Columbia at 

RM 74.6; and (3) a small section of the river referred to as a 

“transitional zone” connecting the braided and the meander 

reaches. Typically, the transitional zone occurs between 

RM 156.9 and RM 151.9 depending on the extent of the 

backwater from Kootenay Lake (Federal Register, 2008). 

Bathymetric Data Collection Areas for 

Water Year 2011

Bathymetric data were collected within an 11-mi reach 

of previously unmapped areas in the meander reach to obtain 

high-resolution bathymetric data. The extent of the surveys 

was from RM 134 to 142 (fig. 3A) and RM 149 to 152 

(fig. 3B). 

Bathymetric data were collected in the Shorty’s Island 

and Myrtle Creek substrate enhancement study area in 

the meander reach. The extent of these surveys was near 

RM 143.5 and 142.9 near Shorty’s Island and at RM 146 near 

the Myrtle Creek confluence with the Kootenai River (fig. 4). 

The data-collection efforts described in this report are part 

of a long-term monitoring program to identify the spatial 

and temporal distribution of sand in the stream channel. This 

baseline survey was initiated to survey both the short- and 

long-term distribution of sediment in the study area. The 

planned survey lines were created as both cross sections and 

longitudinal lines intended to be surveyed bi-annually as part 

of the long-term monitoring program. 

Bathymetric data were collected within the braided reach 

as part of a long-term monitoring program. The extent of these 

surveys was near RM 152.2 near Ambush Rock upstream to 

approximately RM 159.1 downstream of the confluence of the 

Moyie River with the Kootenai River (fig. 5). The bathymetric 

data were collected at 17 cross sections to monitor aggradation 

and degradation of the channel bed to support on-going river 

restoration efforts in the braided reach. 
Introduction 3 tac12-0746_fig01

00 40 20 60 KILOMETERS

20 40 60 MILES

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

Creek Lake

Kootenay

River

Moyie River

River

Yaak

River

Kootenai

River

Kootenay

Lake

Koocanusa

River Mary St.

Fisher

West

Arm

Kootenay

Lake

Columbia

River

Columbia

Lake

River

Tobacco

Slocan

Lake

River

Slocan

River

Libby

Dam

Lake

Creek

Dam

Kootenai

Falls

Dam

Moyie

Dam

Corra

Lynn

Dam

Bonners

Ferry

Shorty’s Island

Troy Libby

Creston

Porthill

Castlegar

Crossport

Moyie Springs

Copeland

Kimberley

Cranbrook

Grohman

Narrows

Queens Bay

Bonnington Falls

Proctor

Nelson

Bonner County

Boundary County

117° 116° 115° 

118° 

49°

50° 

PURCELL

MOUNTAINS

SELKIRK

MOUNTAINS

CABINET

MOUNTAINS

R O C K Y

M O U N T A I N S

S A L I S H

M O U N T A I N S

RM 80 

RM 100

RM 90

RM 140

RM 120

RM 130

RM 110

RM 180

RM 160

RM 170 RM 150

RM

190 RM 200

RM 220

RM 210

08NH064

08NH067 or

12322500

12301933

12305000

12314000

EXPLANATION

Study reach River mile Streamflow-gaging station and No.

RM160

08NH064

+

CANADA

UNITED

STATES

Kootenai River

Drainage Basin

BRITISH

COLUMBIA

IDAHO

IDAHO

IDAHO

MONTANA

CANADA

UNITED STATES

12322000

12310100

12309500

Figure 1. Location of study area in the Kootenai River drainage basin, northern Idaho.
4 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

tac12-0746_fig02

1

95

95

2

2

2

95

Shorty's/Myrtle 

substrate 

enhancement 

project

Meander 

bathymetry

(RM 149–151)

Braided 

cross

sections

Meander 

bathymetry

(RM 134–142)

Porthill

Copeland

Kootenai

Valley

Bonners

Ferry

Moyie

Springs

Leonia

Crossport

MONTANA

IDAHO

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

Shorty’s

Island

Kootenai

River

Moyie River

Purcell

Range

Moyie

Dam

Cabinet Range

Ambush

Rock

Mission

Hill

136.7

139.8 140.4

142.9

146

149.1

152.2 155.3

 158.4 161.6

164.7

133.6

130.5

127.4

167.8

 170.3

124.3 121.2

118.1

114.9

111.8

108.7

105.6

108.1

107.5 106.8 106.2

111.2 110.6

110

109.4

115.6

114.3 113.7

113.1

112.5

117.4

118.7

120.5

119.9

119.3

116.8

116.2

123.6

126.8 126.1

124.9 125.5

122.4 123

121.8

131.1

129.2 129.9

128

128.6

136.1

135.5

134.8 134.2 133

132.3

131.7

138.6

139.2

137.9

137.3

141.7 142.3

141

145.4

148.5

147.9

147.3

146.6 144.8

144.2 143.5

151.9

154.7 153.5 154.1

152.9 151 150.4

149.7 156

156.9

157.2 157.8

159.1 159.7

160.3

160.9 162.2

162.8

163.4

164

165.3165.9

166.5

167.1

168.4

169

169.6

170.9

171.5

Klockmann Ranch

12314000

Tribal

Hatchery

12310100

Bonners

Ferry

12309500

Porthill

12322000

Leonia

12305000

48°

55'

48°

50'

48°

45'

48°

40'

48°

35'

49° 116°30’ 116°25’ 116°20’ 116°15’ 116°10’ 116°05’

Base from U.S. Geological Survey digital data, 1:100,000, 1980. 

Albers equal-area projection: standard parallels 43° 30' and 47° 30',

central meridian -114° 00', latitude of origin 41° 45', 

no false easting or false northing.

EXPLANATION

Canyon reach

Kootenai River white sturgeon 

critical habitat

Braided reach

Meander reach

Transition zone

Streamflow-gaging station 

and No.

135.5 River miles

Leonia

12305000

0

210 543 6 7 MILES

21 3 4 65 7 KILOMETERS

Figure 2. Location of the Kootenai River white sturgeon critical habitat in the study reach, near Bonners Ferry, Idaho.
Introduction 5

tac12-0746_fig03a

RM 134

RM 142

116°28' 116°26' 116°24' 116°22' 116°20' 116°18'

48°

50'

48°

48'

48°

46'

95

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 

photography. Coordinate system: Albers equal-area projection: standard parallels 43° 30' 

and 47° 30', central meridian -114° 00', latitude of origin 41° 45', no false easting or false 

northing; North American Datum of 1983. 0

0 1 2 MILES

1 2 KILOMETERS

Montana

Idaho

Washington

Kootenai R

Saint Joe R

Spokane R

Clark Fork

Pend Oreille R

Columbia R

Map

area

USA

A. Canada River miles 134–142

Figure 3. Extent of the surveys in unmapped portions of the meander reach, near Bonners Ferry, Idaho, water year 2011.
6 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

tac12-0746_fig03b

RM 152

RM 149.0

Bonners

Ferry

2

95

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 

photography. Coordinate system: Albers equal-area projection: standard parallels 43° 30' 

and 47° 30', central meridian -114° 00', latitude of origin 41° 45', no false easting or false 

northing; North American Datum of 1983.

116°24' 116°23' 116°22' 116°21' 116°20' 116°19'

48°

43'

48°

42'

48°

41'

0

0 1 MILES

1 KILOMETERS

Montana

Idaho

Washington

Kootenai R

Saint Joe R

Spokane R

Clark Fork

Pend Oreille R

Columbia R

Map

area

USA

B. Canada River miles 149–152

Figure 3.—Continued
Introduction 7

tac12-0746_fig04

Myrtle Creek

38

18

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 

photography. Coordinate system: Albers equal-area projection: standard parallels 43° 30' 

and 47° 30', central meridian -114° 00', latitude of origin 41° 45', no false easting or false 

northing; North American Datum of 1983.

116°26' 116°25' 116°24' 116°23' 116°22'

48°

46'

48°

45'

0

0 1 MILES

1 KILOMETERS

Survey locations

EXPLANATION

Montana

Idaho

Washington

Kootenai R

Saint Joe R

Spokane R

Clark Fork

Pend Oreille R

Columbia R

Map

area

USA

Canada

Shorty's 

Island

Figure 4. Extent of the Shorty’s Island and Myrtle Creek substrate enhancement study area, near Bonners Ferry, Idaho, water 

year 2011.
8 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

tac12-0746_fig05

Bonners

Ferry

Moyie

Springs

2

95

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 

photography. Coordinate system: Albers equal-area projection: standard parallels 43° 30' 

and 47° 30', central meridian -114° 00', latitude of origin 41° 45', no false easting or false 

northing; North American Datum of 1983.

116°20' 116°18' 116°16' 116°14' 116°12'

48°

44'

48°

42'

48°

40'

0 1

0 1 2 MILES

2 KILOMETERS

Survey locations

EXPLANATION

Montana

Idaho

Washington

Kootenai R

Saint Joe R

Spokane R

Clark Fork

Pend Oreille R

Columbia R

Map

area

USA

Canada

Ambush

Rock

Moyie River

Figure 5. Extent of the braided reach cross-section survey area, near Bonners Ferry, Idaho, water year 2011.
Methods 9

Methods

The bathymetric data were collected using a multibeam 

echosounder (MBE) system mounted on a USGS-owned and 

operated 25-foot jet boat research vessel. The echosounding 

component was a 240 kHz ODOM ES3 multibeam 

echosounder capable of projecting 120, 240, or 480 beams 

spanning a max of 120° swath (width of coverage). Figures 6

and 7 show examples of how the multibeam echosounder 

collects the corrected elevation point coverage across the 

survey swath. For the surveys on the Kootenai, 240 beams 

were selected and the port and starboard angles were limited 

to 50° per side for a total angular coverage of 100°. 

A Teledyne TSS DMS-10 dynamic motion reference 

unit accounted for heave, pitch, and roll of the vessel. Two 

Digibar Pro sound velocity probes (velocimeters) were used 

to profile the speed of sound underwater. One velocimeter was 

mounted and operated real-time near the MBE to account for 

spatial change in the surface speed of underwater sound. The 

second velocimeter was used to acquire a depth profile that 

recorded how the speed of underwater sound varied by depth. 

A Trimble® R8 GPS receiver mounted over the MBE was 

radio linked to another GPS receiver set over a survey control 

point on land to provide real-time horizontal and vertical 

positioning. A Hemisphere® VS111 dual-GPS system was 

used for the heading and to output a 1 pulse per second (1PPS) 

output. The entire MBE system is shown in figures 7 and 8.

An ODOM® Real-Time Appliance (RTA) was used 

to time stamp the MBE, motion reference unit, real-time 

velocimeter, RTK-GPS positioning and elevation, and precise 

heading data to within 1 millisecond based on the 1PPS 

signal from the Hemisphere® VS111. The RTA output the 

bathymetric data to two laptops, one for data acquisition 

and one for data processing. In addition, a Hummingbird®

side-scan was used for qualitative purposes to verify and note 

unique features (trees, sunken cars, sand dunes, clay steps and 

benches) to the channel bathymetry. A daily field log of the 

bathymetric surveys was kept to record the equipment used, 

crew members, referenced survey bench marks, sound velocity 

profiles, file names, and other ancillary information. An 

example of the daily log is provided in appendix A. Figure 9

shows an image of each of these components.

The bathymetric data were collected in the field using 

the HYPACK® software HYSWEEP®. The raw data were 

then edited using HYPACK®’s MBMAX software. All raw 

data were initially filtered to exclude the outer 10° of the 

multibeam swath. These data were out of tolerance (see 

section, “Quality Assurance”) and therefore excluded from the 

final data. The edited data were reduced to a 3×3-foot cell size 

as XYZ ASCII data using HYPACK® Combined Uncertainty 

and Bathymetric Estimator (CUBE). Two hundred and forty 

beams were used for the survey and overlap of adjacent 

survey lines was between 75 and 100 percent. However, 

areas of missing data referred to as holidays occurred within 

the dataset due to the filtering of macrophytes, editing of 

erroneous data points, and areas where it was too shallow to 

allow complete coverage. 

Quality Assurance and Quality Control 

Quality assurance (QA) and quality control (QC) are 

critical with MBE surveys to maintain the highest degree of 

accuracy. Qualitative notes documenting anything that might 

affect the quality of the data, such as wave action, macrophyte 

growth, poor GPS quality, and any other observation that 

could degrade the bathymetric data were recorded in the daily 

field log. 

Quality Assurance

Prior to and during the survey, unique tasks were 

conducted at specified intervals to prepare the MBE system 

for bathymetric surveying, but also to describe the total 

estimated error within the system. Tasks and descriptions are 

shown in table 1 for the recommended measurement interval 

for each project and were developed based on requirements 

from U.S. Army Corps of Engineers (2004), National Oceanic 

and Atmospheric Administration (2011), and system specific 

requirements. The order of tasks shown in table 1 is important 

because each task is dependent on the preceding task. Qualityassurance elements were developed following the input 

requirements of the Total Propagated Uncertainty (TPU) 

feature built into HYPACK® software. The TPU required a 

description of the general, environmental, and sensor settings 

to best estimate the total error potential in the survey data. 

A table of the procedures used for this survey is provided in 

appendixes B and C.

Perhaps the most significant quality-assurance element is 

the patch test (table 1). A patch test included running a series 

of MBE survey lines to compensate for physical mounting 

differences including latency, pitch, roll, and yaw (fig. 10). 

Two patch tests were conducted before and after the surveys 

to ensure the MBE system was correctly offset and calibrated 

(appendixes D and E). A complete description of the patch 

test process can be found in U.S. Army Corps of Engineers 

(2004) and National Oceanic and Atmospheric Administration 

(2011). The offsets from the patch test were applied to the 

system prior to the surveys on the Kootenai River. A second 

patch test was conducted after the Kootenai River bathymetric 

surveys to ensure the system was still properly aligned and no 

adjustments to the offset coefficients were necessary. Neither 

of the patch tests were completed on the Kootenai River, due 

to the poor channel geometry and river currents that are not 

appropriate for a patch test.
10 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

tac12-0746_fig06

Depth (D)

NADIR

Swath

≈2*tan(50)*D

50°

100°

0.0

10.0

20.0

-20.0 0.0 20.0

Figure 6. Example of the angular coverage and number of beams for the multibeam echosounder.
Methods 11

tac12-0746_fig07

RTK-GPS

Heading GPS Heading GPS 

Multibeam echosounder, 

velocimeter, and motion 

reference unit 

(see figure 8)

Figure 7. Multibeam echosounder components and mount on USGS research vessel.
12 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

tac12-0746_fig08

Multibeam 

echosounder Velocimeter

Motion reference unit 

(hidden from view)

Figure 8. Close-up view of the submerged components of the multibeam echosounder.
Methods 13

Figure 9. Data acquisition, processing, and display components for the MBE system.

tac12-0746_fig10

RTK-GPS controller

Hummingbird® 

side-scan

Data processing PC Data aquisition PC

Daily field log

Hemisphere® VS111 dual-GPS receiver

ODOM® Real-Time Appliance
14 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Table 1. Project quality assurance and quality control elements for multibeam bathymetric surveys.

Task Recommended interval Measurement precision Summary

RTK-GPS horizontal 

and vertical control

1 / project 3rd order or better Prior to the start of the survey, a reconnaissance survey should occur to verify and/or establish proper vertical and 

horizontal control within the survey area. If necessary, allow 3 weeks to allow precise ephemeris results for static surveys in areas with no existing horizontal and/or vertical control. The accuracy for the horizontal and vertical control order should be clearly stated as well as the coordinate system used (State Plane preferred, then UTM).

Multibeam echosounder 

general settings

1 / project Varies The general settings include but are not limited to Angular Coverage, ping rate, beam width, pulse length, steering 

angle, frequency, and bandwidth. Each of these should be noted from the manufacturer.

Environmental settings 1 / project Varies A general estimate for the following should be approximated prior to each project: speed of sound, peak-to-peak 

swell, forward-aft seafloor slope, port-starboard seafloor slope, water level uncertainty, spatial tide prediction uncertainty, sound speed sensor uncertainty (real-time, cast, spatial-temporal variation, thickness of spatialtemporal layer, uncertainty beyond profile, and max depth of SV profile). 

MBES sensor offset 

measurements and uncertainty estimates

1 / project Varies The physical offsets (Foreword, starboard, and vertical) for each of the MBES components (RTK-GPS, MRU, 

and multibeam echosounder) should be measured each time a component is installed. 

A verification of these 

measurements should occur at the beginning of each project.

Sound velocity probe 

calibration

1 / project ±1 foot per second Each echosounder is required to be factory-calibrated once per year. Prior to each project, each sound velocity 

probe should be verified that the sound velocity values match the factory-calibration values.

Vessel survey speed limitation 1 / project ± 1 knot A qualitative estimate for a proper survey speed should be considered prior to the start of each survey. The proper 

survey speed should take the following into consideration, 1.survey depths, 2.river currents. Slower survey speeds will likely be necessary in areas of higher depths (> 40 feet) and on rivers with high velocities. Under normal conditions, a survey speed ranging from 5 to 7 knots is appropriate.

Multibeam beam-width 

limitations

1 / project Varies (degrees) Beam width restrictions (°) may be required in deeper water where the quality of the outer beams may exceed . 

This will be decided by the results of the performance test in section, “Quality Assurance.”

Overlapping requirement 1 / project Varies (%) Overlapping requirements (percent coverage) should be decided prior to the start of the project and is a function of 

the style of survey. 

Bar check verification 1 / project ± 0.05 foot A bar check should occur once per project to verify the NADIR depth of the multibeam. This can be verified using 

a rectangular surface that is lowered a known depth and running the bar check utility within HYSWEEP Survey. In addition, a manual check should be made using the GPS, vertical antenna offsett, and depth calculation to verify the estimated corrected depth of the MBES. 

Patch test 2 / project Varies A patch test should be surveyed prior to the start of each project. It is important that the sound velocity calibration 

and H/V control limitations have been established prior to the patch test as they could affect the outcome of the test. After each project, a follow-up patch test should occur in the same location using the same lines to verify the first patch test to ensure no changes were incurred during the project. If any physical or equipment changes are made during the project, a new patch test should be surveyed to account for any potential changes this might have to the system. 

Horizontal and vertical 

verification check

1 / day ± 0.01 foot The horizontal position and vertical elevation verification should occur daily to explain the spatial accuracy of the 

multibeam system. The horizontal position (X,Y) and vertical elevation (Z) verification can be can be completed using the RTK-GPS to verify an existing or established benchmark in the study area. 

Velocity casts 2–3 / day ± 0.01 foot A velocity cast should occur prior to the survey each day. A second cast should be taken approximately half-way 

through the day. A third cast should be taken at the end of the day. The frequency of the velocity casts should be increased in areas with a significant stratification. Each of the velocity casts should be loaded into the editing file so that changed to the velocity profile is accounted for during the survey.
Methods 15

Figure 10. Patch test lines and resulting bathymetry from Lake Coeur d’Alene near Cougar Bay, Idaho.

tac12-0746_fig11

2,080

2,083

2,070

2,060

2,050

2,040

2,030

2,020

2,012

Corrected bed elevation, 

in feet

EXPLANATION

B.HSX

C.HSX

BA.HSX

A.HSX

CA.HSX

CE.HSX

CD.HSX

AF.HSX

CC.HSX

AE.HSX

AD.HSX

CB.HSX

AC.HSX

AA.HSX

B

C

A

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 

photography. Coordinate system: Albers equal-area projection: standard parallels 43° 30' 

and 47° 30', central meridian -114° 00', latitude of origin 41° 45', no false easting or false 

northing; North American Datum of 1983.

Montana

Idaho

Washington

Kootenai R

Saint Joe R

Spokane R

Clark Fork

Pend Oreille R

Columbia R

Map

area

USA

Canada

0 100 200 300 400 500 FEET

0 50 100 150 METERS

CC.HSX

C

Actual surveyed lines

Planned lines

Roll test lines

Yaw lines

Pitch lines

Latency lines
16 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Quality Control

Following the adjustments from the patch test, a 

performance test (also referred to as a beam angle check) 

provided quality control by quantifying the accuracy of 

the MBE (fig. 11). The performance test compared a set of 

standard survey data against a known reference surface. The 

reference surface was created by surveying 10 lines (5 parallel 

and 5 perpendicular) spaced equal to the depth creating 

200 percent overlap and edited to remove any data outside of 

45° from the NADIR beam. The final reference surface is the 

best representative surface for a baseline measure to check the 

performance of the system. Two standard survey lines were 

surveyed across the center of the reference surface to be used 

as the performance measure. The standard survey lines were 

edited using the same methods applied to all data collected. 

The performance test for the Kootenai River bathymetric 

surveys was conducted on April 28, 2011, at Lake Coeur 

d’Alene, Idaho. It was recommended that the performance 

test be done on the same body of water as the study, but there 

was not a suitable location within the Kootenai River for 

the performance test. The output from the performance test 

includes a summary of how the accuracy of the X,Y, and Z 

data are distributed through the swath of the MBE. Typically, 

the integrity of the data is diminished as it deviates from the 

center (NADIR) beam. The results of the performance test 

were compared with the minimum performance standards 

as defined by U.S. Army Corps of Engineers (2004) and are 

shown in appendix F.

An additional output option from the HYPACK® CUBE 

module used for quality control is the estimated uncertainty. 

The uncertainty was estimated for each of the estimated 

gridded surfaces, for this study a 3×3-foot grid (table 2). Each 

estimated grid elevation was estimated based on the most 

statistically significant elevation within the grid. The total 

number of data points used to develop the grid output were 

highly variable and depended on the distance from NADIR 

(decreasing density from NADIR), depth of water (decreasing 

density with increasing depth), and amount of overlapping 

data (increasing density with increasing overlap). 

Table 2. Quality-control results.

[Data-quality objectives: Hard bottom, soft bottom, and other surveys and studies were taken from U.S. Army Corps of Engineers (2002; table 3-1, Corps 

Accuracy Standards, Quality control, and Quality Assurance Requirements]

Performance 

standard

Data-quality objectives (±) ft Quality-control results (±) ft

Hard 

bottom

Soft 

bottom

Other 

surveys 

and studies

Multibeam 

echosounder 

bathymetric 

survey in 

meander reach

Substrate 

Enhancement 

Project near 

Shorty’s Island and 

Myrtle Creek

Braided reach 

cross-section 

monitoring 

surveys

Resultant elevation accuracy (95%)

depth < 15 ft 0.5 0.5 1.0 0.5–0.64 0.5–0.7 0.48

15 ft < depth ≤ 40 ft 1 1.0 2.0 NA

depth > 40 ft 1 1.0 2.0 NA

Horizontal Positioning System 

Accuracy (ft)

< 6 6.0 16.0 <1 <1 <1

Supplemental control accuracy

Horizontal 3rd order 3rd order 3rd order 2nd order 2nd order 2nd order

Vertical 3rd order 3rd order 3rd order 2nd order 2nd order 2nd order

Minimum survey coverage density 100% Sweep 200 ft 500 ft ≈ 100% Sweep NA NA
Methods 17

tac12-0746_fig11

2,080

2,083

2,070

2,060

2,050

2,040

2,030

2,020

2,012

Depth of water, in feet

EXPLANATION

E.HSX

D.HSX

CG.HSX

CF.HSX

BB.HSX

AG.HSX

003_0827.HSX

003_0818.HSX

004_0820.HSX

002_0816.HSX

005_0823.HSX

001_0814.HSX

AH.HSX

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 

photography. Coordinate system: Albers equal-area projection: standard parallels 43° 30' 

and 47° 30', central meridian -114° 00', latitude of origin 41° 45', no false easting or false 

northing; North American Datum of 1983.

0 100 200 300 400 FEET

0 50 100 METERS

Montana

Idaho

Washington

Kootenai R

Saint Joe R

Spokane R

Clark Fork

Pend Oreille R

Columbia R

Map

area

USA

Canada

EXPLANATION

004_0820.HSX

Planned lines

Raw lines

Figure 11. Performance Test reference lines, standard lines, and resulting bathymetry from Lake Coeur d’Alene near Cougar 

Bay, Idaho.
18 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Bathymetric Survey 

Data 

Edited raw data are presented 

in a generic ASCII XYZ format in 

the most raw form so that it can be 

used in various types of geospatial 

software applications. The digital 

elevation data were projected 

using UTM Zone 11 North, North 

American Datum of 1983 (NAD 

83) units of U.S. feet and the North 

American Vertical Datum of 1988 

units of U.S. feet. Tables 3, 4, and 5

present a description of the MBE 

bathymetric data from each of the 

three survey areas. A thorough 

description and ASCII XYZ data are 

provided in the metadata for each 

survey area.

Multibeam Echosounding 

Survey in Meander Reach

Single-beam echosounder (SBE) 

bathymetric data were collected 

within this reach in 2002 (Barton and 

others, 2004), but did not provide 

a full coverage of the channel 

bottom. SBE bathymetry is not as 

desirable as multibeam echosounder 

(MBE) bathymetry for use in twodimensional flow models. The MBE 

data will be used to update the 

bathymetric surfaces used to develop 

and update one- and two-dimensional 

flow models. In addition, the data 

provided a nearly continuous surface 

that could aid in the delineation 

of sediment facies features in 

the river, such as lacustrine clay, 

bedrock, sand, scour holes, and other 

geomorphic features that are useful 

in describing the known habitat 

for the white sturgeon. The extent 

of the survey coverage and MBE 

bathymetry are presented in table 3.

Table 3. Multibeam echosounder bathymetric survey in meander reach.

[River mile indicates a 1-mile reach beginning at the River Mile number. Data and metadata can be accessed at 

http://water.usgs.gov/lookup/getspatial?ds694_meander_reach_2011]

Survey 

extent Image Survey date

File 

name

River Mile 151 05-19-2011 RM151.xyz

River Mile 150 05-19-2011 RM150.xyz

River Mile 149 05-12-2011 RM149.xyz

River Mile 141 05-3-2011 RM141.xyz

River Mile 140 05-3-2011 RM140.xyz
Bathymetric Survey Data 19

Survey 

extent Image Survey date

File 

name

River Mile 139 05-04-2011 to 

05-05-2011

RM139.xyz

River Mile 138 05-5-2011 RM138.xyz

Table 3. Multibeam echosounder bathymetric survey in meander reach—Continued.

[River mile indicates a 1-mile reach beginning at the River Mile number. Data and metadata can be accessed at http://water.usgs.gov/

lookup/getspatial?ds694_meander_reach_2011]
20 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Survey 

extent Image Survey date

File 

name

River Mile 137 05-31-2011 RM137.xyz

River Mile 136 06-1-2011 RM136.xyz

Table 3. Multibeam echosounder bathymetric survey in meander reach—Continued.

[River mile indicates a 1-mile reach beginning at the River Mile number. Data and metadata can be accessed at http://water.usgs.gov/

lookup/getspatial?ds694_meander_reach_2011]
Bathymetric Survey Data 21

Survey 

extent Image Survey date

File 

name

River Mile 135 06-01-2011 to 

06-02-2011

RM135.xyz

River Mile 134 06-2-2011 RM134.xyz

Table 3. Multibeam echosounder bathymetric survey in meander reach—Continued.

[River mile indicates a 1-mile reach beginning at the River Mile number. Data and metadata can be accessed at http://water.usgs.gov/

lookup/getspatial?ds694_meander_reach_2011]
22 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Table 4. Substrate enhancement project near Shorty’s Island and Myrtle Creek.

[Data and metadata can be accessed at http://water.usgs.gov/lookup/getspatial?ds694_substrate_enhancement_2011]

Survey

extent Link to map image Surveydate File name

Myrtle Creek and Shorty’s Island 05-18-2011 Substrate_Enhancement_Project_

bathymetry_May_2011

Myrtle Creek and Shorty’s Island 07-12-11 to 

07-13-2011

Substrate_Enhancement_Project_

bathymetry_July_2011

Substrate Enhancement Project near Shorty’s Island and Myrtle Creek

The cross-sections and longitudinal profiles were surveyed on the ascending (May) and descending 

(July) limbs of the spring runoff hydrograph. The extent of the survey coverage and MBE bathymetry are 

presented in table 4.
Bathymetric Survey Data 23

Table 5. Braided reach cross-section monitoring surveys.

[Data and metadata can be accessed at http://water.usgs.gov/lookup/getspatial?ds694_braided_reach_2011]

Survey

extent Lind to map image Survey date File name

Braided reach 

cross sections

 05-16-2011 to 

 05-17-2011

KR2011_BraidedXSections_May.xyz

 07-12-2011 KR2011_BraidedXSections_July.xyz

Braided Reach Cross-Section Monitoring Surveys

The survey included two survey periods: 

1. Ascending limb of the high spring flows in May, and 

2. Descending limb of the high spring flows in July and August 2011. 

The extent of the survey coverage and MBE system bathymetry are presented in table 5.
24 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Acknowledgments

The author expresses appreciation to the Kootenai 

Tribe of Idaho and to the Bonneville Power Administration 

for funding and logistical support during the bathymetric 

surveys. The author also would like to thank all USGS Idaho 

Water Science Center colleagues for their assistance with 

data collection.

References Cited

Barton G.J., Moran E.H., and Berenbrock, C., 2004, Surveying 

cross sections of the Kootenai River between Libby Dam, 

Montana, and Kootenay Lake, British Columbia, Canada: 

U.S. Geological Survey Open-File Report 2004–1045, 

35 p., accessed August 3, 2012, at http://id.water.usgs.gov/

PDF/ofr041045/.

Boundary County Historical Society, 1987, The history 

of Boundary County, Idaho: Portland, Oregon, Taylor 

Publishing Company, p. 43–46 and 48.

Federal Register, 1994, Endangered and threatened wildlife 

and plants—Determination of endangered status for the 

Kootenai River population of the white sturgeon: Federal 

Register, v. 59, no. 171, p. 45,989-46,002, accessed 

April 27, 2012, at http://ecos.fws.gov/docs/federal_register/

fr2678.pdf. 

Federal Register, 2008, Endangered and threatened wildlife 

and plants—Critical habitat revised designation for 

the Kootenai River population of the white sturgeon 

(Acipenser transmontanus): Federal Register, v. 73, no. 132, 

p. 39,505–39,523, accessed April 27, 2012, at http://

www.gpo.gov/fdsys/pkg/FR-2008-07-09/pdf/E8-15134.

pdf#page=1.

Kock, T.J., Congleton, J.L., and Anders, P.J., 2006, Effects 

of sediment cover on survival and development of white 

sturgeon embryos: North American Journal of Fisheries 

Management, v. 26, no. 1, p. 134–141.

Kootenai Tribe of Idaho, 2009, Kootenai River Habitat 

Restoration Project Master Plan: Kootenai Tribe of Idaho, 

291 p., accessed April 27, 2012, at http://www.kootenai.org/

fish_restoration.html. 

National Oceanic and Atmospheric Administration, 2011, 2011 

Field procedure manual: National Oceanic and Atmospheric 

Administration, 333 p., accessed April 27, 2012, at http://

www.nauticalcharts.noaa.gov/hsd/fpm/fpm.htm. 

Paragamian, V.L., Kruse, Gretchen, and Wakkinen, Virginia, 

2001, Spawning habitat of Kootenai River white sturgeon, 

post-Libby Dam: North American Journal of Fisheries 

Management, v. 21, no. 1, p. 22–33.

Paragamian, V.L., Wakkinen, V.D., and Kruse, Gretchen, 2002, 

Spawning locations and movement of Kootenai River white 

sturgeon: Journal of Applied Ichthyology, v. 18, p. 608–616.

Partridge, F., 1983, Kootenai River fisheries investigations: 

Boise, Idaho Department of Fish and Game, Job 

Completion Report, Project F-73-R-5, Subproject IV, 

Study IV.

Redwing Naturalists, 1996, History of diking on the Kootenay 

River floodplain in British Columbia: Report of Redwing 

Naturalists to Habitat Enhancement Branch, Department of 

Fisheries and Oceans, British Columbia, Canada, p. 17–14, 

and 20–22.

Turney-High, H.H., 1969, Ethnography of the Kutenai: New 

York, Kraus Reprint Company, p. 44.

U.S. Army Corps of Engineers, 2004, Engineering and Design, 

Hydrographic surveying, EM 1110-2-1003, Change 1: 

Washington, DC, U.S. Army Corps of Engineers, accessed 

August 3, 2012, at http://140.194.76.129/publications/engmanuals/EM_1110-2-1003_pfl/toc.htm. 

U.S. Fish and Wildlife Service, 1999, Recovery plan for 

the white sturgeon (Acipenser transmontanus): Kootenai 

River population: U.S. Fish and Wildlife Service, Portland, 

Oregon, 96 p. plus appendixes, accessed April 27, 2012, at 

http://ecos.fws.gov/docs/recovery_plan/990930b.pdf.

U.S. Fish and Wildlife Service, 2006, Fish and Wildlife 

Service biological opinion regarding the effects of Libby 

Dam operations on the Kootenai River white sturgeon, 

bull trout, and Kootenai sturgeon critical habitat: Fish and 

Wildlife Service Biological Opinion, 1-9-01-F-0279R, 

153 p. 
Appendixes 25

Appendixes

Appendixes are presented as Microsoft© Excel spreadsheets and can be accessed and downloaded at 

http://pubs.usgs.gov/ds/694/.

Appendix A. Daily Logs.

Appendix B. Quality Control Parameters Defined for Estimating Total Propagated Uncertainty.

Appendix C. Multibeam Echosounder Physical Offsets.

Appendix D. Patch Test, April 28, 2011.

Appendix E. Patch Test, June 15, 2011.

Appendix F. Performance Test, April 28, 2011.
26 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

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

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Boise, Idaho 83702

http://id.water.usgs.gov
Fosness—Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011—Data Series 694