Bathymetric Surveys of the Kootenai River Near Bonners Ferry, Idaho—Water Year 2011

Prepared in cooperation with the Kootenai Tribe of Idaho Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Data Series 694

U.S. Department of the Interior U.S. Geological Survey 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 extending from river mile (RM) 159.7, downstream of the Moyie River, to RM 141.7 in the meander reach downstream In 2009, the Kootenai Tribe of Idaho released and of Shorty’s Island (Federal Register, 2008). implemented the Kootenai River Habitat Restoration Master Historical references indicate that dikes were built on Plan. This plan aimed to restore, enhance, and maintain natural levees early in the 20th century to protect agricultural the Kootenai River habitat and landscape to support and areas in the Kootenai River floodplain from flooding sustain habitat conditions for aquatic species and animal (Turney‑High, 1969; Boundary County Historical Society, populations. In support of these restoration efforts, the U.S. 1987; Redwing Naturalists, 1996). Changes to the natural Geological Survey, in cooperation with the Kootenai Tribe river environment have led to detrimental conditions in the of Idaho, conducted high-resolution multibeam echosounder critical habitat reach. Additionally, the construction and bathymetric surveys in May, June, and July 2011, as a baseline operation of Libby Dam, put into service in 1972, substantially bathymetric monitoring survey on the Kootenai River near altered Kootenai River streamflow and water quality, and Bonners Ferry, Idaho. Three channel patterns or reaches exist created a habitat unsuitable to sustain natural recruitment of in the study area—braided, meander, and a transitional zone the Kootenai River white sturgeon (U.S. Fish and Wildlife connecting the braided and meander reaches. Bathymetric Service, 2006). Research by the Idaho Department of Fish and data were collected at three study areas in 2011 to provide: Game on sturgeon populations determined that there was a (1) surveys in unmapped portions of the meander reach; lack of juvenile sturgeon in all but four 1-year classes during a (2) monitoring of the presence and extent of sand along 16-year period (Partridge, 1983). planned lines within a section of the meander reach; and In 1994, the U.S. Fish and Wildlife Service (USFWS) (3) monitoring aggradation and degradation of the channel listed the Kootenai River population of white sturgeon as an bed at specific cross sections within the braided reach and endangered species under the provisions of the Endangered transitional zone. The bathymetric data will be used to update Species Act of 1973, as amended. The population was listed and verify flow models, calibrate and verify sediment transport as endangered because of decreasing numbers and a lack of modeling efforts, and aid in the biological assessment in juvenile recruitment that was first noted in the mid-1960s support of the Kootenai River Habitat Restoration Master (Federal Register, 1994; U.S. Fish and Wildlife Service, Plan. The data and planned lines for each study reach 1999). Many researchers attributed these decreasing numbers were produced in ASCII XYZ format supported by most and lack of recruitment to the degradation of white sturgeon geospatial software. 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 Introduction outlined in the Kootenai River white sturgeon recovery plan (U.S. Fish and Wildlife Service, 2006). One proposed Anthropogenic influence to the Kootenai River (or improvement was, “a flow regime that limits sediment Kootenay for the Canadian areas) is evident upstream deposition and maintains appropriate rocky substrate for of, within, and downstream of the federally designated sturgeon egg adhesion, incubation, escape cover, and free critical‑habitat reach of the Kootenai River population of embryo development…” (Federal Register, 2008, p. 39,513 white sturgeon (Acipenser transmontanus). The Kootenai and 39,522). River white sturgeon critical habitat is a 18 mi long reach 2 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

In 2009, the Kootenai Tribe of Idaho released and patterns (hereinafter referred to as “reaches”) are in the study implemented the Kootenai River Habitat Restoration Master area: (1) A braided channel, consisting primarily of a gravel Plan (hereinafter referred to as the “Master Plan”). The goal and cobble substrate, extending from RM 159.7 near the of the Master Plan is to restore, enhance, and maintain the confluence of the Moyie River downstream to RM 152.9 near Kootenai River habitat and landscape so that it supports and Bonners Ferry; (2) a meandering channel, primarily consisting sustains habitat conditions for aquatic species and animal of sand and lacustrine clay, extending from RM 152.9 populations (Kootenai Tribe of Idaho, 2009). In support of downstream approximately 78 mi to the confluence of the these restoration efforts, the U.S. Geological Survey (USGS), Kootenai River with Kootenay Lake in British Columbia at in cooperation with the Kootenai Tribe of Idaho conducted RM 74.6; and (3) a small section of the river referred to as a bathymetric surveys of the Kootenai River during May, June, “transitional zone” connecting the braided and the meander and July 2011, as a baseline monitoring survey within the reaches. Typically, the transitional zone occurs between braided and meander reaches of the Kootenai River near RM 156.9 and RM 151.9 depending on the extent of the Bonners Ferry, Idaho. Bathymetric surveys on the Kootenai backwater from Kootenay Lake (Federal Register, 2008). 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 Bathymetric Data Collection Areas for enhancement project; and (3) surveys within the braided reach Water Year 2011 at selected monitoring cross sections. Each of the surveys support short- and long-term adaptive management and Bathymetric data were collected within an 11-mi reach monitoring as part of the Master Plan. of previously unmapped areas in the meander reach to obtain This document presents the bathymetric data from high-resolution bathymetric data. The extent of the surveys each of the three surveys on the Kootenai River for water was from RM 134 to 142 (fig. 3A) and RM 149 to 152 year 2011. A description of the study areas, data-collection (fig. 3B). methods, and quality-control and quality-assurance procedures Bathymetric data were collected in the Shorty’s Island are discussed to describe the data-collection efforts. 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 Description of Study Area the Myrtle Creek confluence with the Kootenai River fig.( 4). The data-collection efforts described in this report are part The Kootenai River is the second largest contributor to of a long-term monitoring program to identify the spatial the Columbia River in terms of discharge volume (fig. 1). and temporal distribution of sand in the stream channel. This From its headwaters in the Rocky, Salish, and Purcell baseline survey was initiated to survey both the short- and Mountains, the Kootenai River flows to the south through long-term distribution of sediment in the study area. The northwestern Montana. Turning west until reaching the base planned survey lines were created as both cross sections and of the Cabinet Mountains, the river then flows north through longitudinal lines intended to be surveyed bi-annually as part the Kootenai Valley of northern Idaho. From there, the river of the long-term monitoring program. reaches its terminus at Kootenay Lake in British Columbia, Bathymetric data were collected within the braided reach Canada, at the base of the Selkirk Mountains. In 1972, the as part of a long-term monitoring program. The extent of these U.S. Army Corps of Engineers managed the construction of surveys was near RM 152.2 near Ambush Rock upstream to Libby Dam on the upper Kootenai River near Libby, Montana, approximately RM 159.1 downstream of the confluence of the creating Lake Koocanusa. Moyie River with the Kootenai River (fig. 5). The bathymetric The study area described in this report lies within data were collected at 17 cross sections to monitor aggradation those parts of the Kootenai River within the State of Idaho and degradation of the channel bed to support on-going river (fig. 2) including the critical habitat. Three distinct channel restoration efforts in the braided reach. Introduction 3

River

MOUNTAINS 115° 115°

Tobacco

MOUNTAINS SALISH River RM 220 RM

12301933

Lake

Fisher Dam

River Libby Koocanusa

River

ROCKY 210 RM

Libby

MONTANA RM 200 RM

Lake Kootenay

Dam

Falls

190 RM

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

Columbia Kootenai Lake

Creek

River Kootenai

CANADA

River

RM 180 RM

12305000

Dam

Yaak Lake

Creek

UNITED STATES UNITED

Troy

Cranbrook

RM 170 RM

RM 160 RM

Dam

Moyie

RM 140 RM RM 130 RM 116° 116° MOUNTAINS

Mary Moyie River BRITISH

Kimberley Moyie

COLUMBIA

Springs CABINET

St.

RM 120 RM Copeland

MOUNTAINS Crossport Ferry

12314000 RM 100 RM 12309500

Porthill River

Bonners Creston

PURCELL 90 RM

Island

Shorty’s RM 150 RM

12310100 IDAHO

Castlegar Kootenay

12322500

08NH067 or 08NH067

RM 110 RM County Boundary

MOUNTAINS County Bonner RM 80 80 RM

12322000

08NH064

Lake 117° 117°

Proctor SELKIRK Kootenay

Bay

49°

Queens Arm

Nelson

West 60 MILES

River

Columbia

Dam Lynn

River Corra Lake Narrows

Grohman

Slocan 50° 50° Slocan 40 Falls 60 KILOMETERS

Bonnington

IDAHO 118° 118° 40 20 20

0 0

STATES

UNITED CANADA Study reach River mile Streamflow-gaging station and No. EXPLANATION

Kootenai River Kootenai

Drainage Basin Drainage IDAHO RM160 08NH064 L ocation of study area in the Kootenai River drainage basin, northern Idaho .

Figure 1. tac12-0746_fig01 4 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

116°30’ 116°25’ 116°20’ 116°15’ 116°10’ 116°05’ 49° 105.6 Porthill 106.2 107.5 106.8 Porthill 108.1 12322000 EXPLANATION 109.4 108.7 110 111.8 112.5 Kootenai River white sturgeon 111.2 critical habitat 110.6 113.1 Kootenai 114.3 113.7 Transition zone 116.8 114.9 95 115.6 116.2 117.4 1 Meander reach 119.3 118.7 118.1 119.9 Braided reach 48° 120.5 55' 122.4 123 123.6 121.2 Canyon reach 121.8 124.3 Copeland 124.9 Leonia Streamflow-gagingPurcell station 125.5 12305000 126.1 126.8 and No.Range 128 127.4River 135.5 River miles 128.6 129.2 129.9 Kootenai Valley 130.5 131.1 131.7 133.6 132.3 134.2 133 134.8 48° 136.1 50' 135.5 136.7 137.3 Meander 137.9 bathymetry 138.6 (RM 134–142) IDAHO 139.2 140.4 Klockmann Ranch 141 139.8 12314000 141.7 142.3 95

SELKIRK RANGE Shorty’s 142.9 r Island e v MONTANA i R 144.2 143.5 Shorty's/Myrtle e 48° i substrate 144.8 y 45' o 145.4 146.6 Meander enhancement M bathymetry Moyie project 146 Springs 147.3 (RM 149–151) Moyie 2 Dam 147.9 Mission Braided Bonners 158.4 162.8 148.5 Hill Ferry cross 161.6 160.9 149.1 12309500 sections 157.8 162.2 150.4 157.2 163.4 151 156 160.3 149.7 152.9 164 156.9 159.7 159.1 Tribal 151.9 152.2 164.7 Hatchery Ambush 155.3 Crossport 12310100 153.5 154.1 154.7 165.3 166.5 Rock 2 Bonners 165.9 167.1 Ferry 48° 40' 167.8 168.4 Cabinet Range 169 169.6 170.3 170.9 2 171.5 95 Leonia Leonia 12305000

48° 35' Base from U.S. Geological Survey digital data, 1:100,000, 1980. 210 543 6 7 MILES Albers equal-area projection: standard parallels 43° 30' and 47° 30', central meridian -114° 00', latitude of origin 41° 45', 0 21 3 4 65 7 KILOMETERS no false easting or false northing. Figure 2. Location of the Kootenai River white sturgeon critical habitat in the study reach, near Bonners Ferry, Idaho.

tac12-0746_fig02 Introduction 5

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

RM 134

48° 50'

48° 48'

RM 142

48° 46' Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 0 1 2 MILES 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 1 2 KILOMETERS

A. River miles 134–142 Canada USA P Map e R n area K a d i o b O o m r t u e e l i n l a o l i R e C

Cl ar Montana k Fo S r po k kane R Idaho Washington Sai nt Joe R

Figure 3. Extent of the surveys in unmapped portions of the meander reach, near Bonners Ferry, Idaho, water year 2011.

tac12-0746_fig03a 6 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

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

48° 43'

RM 149.0

2 95

48° 42'

RM 152RM 152

Bonners Ferry

48° 41'

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 0 1 MILES 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 1 KILOMETERS

B. River miles 149–152 Canada USA P e R n Map K a d i o b O area o m r t u e e l i n l a o l i R e C

Cl ar Montana k Fo S r po k kane R Idaho Washington Sai nt Joe R

Figure 3.—Continued

tac12-0746_fig03b Introduction 7

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

48° 46' Shorty's Island

48° 45'

Myrtle Creek

Cl ar Montana k Fo S r po k kane R Idaho Washington Sai nt Joe R

Figure 4. Extent of the Shorty’s Island and Myrtle Creek substrate enhancement study area, near Bonners Ferry, Idaho, water year 2011.

tac12-0746_fig04 8 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

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

48° 44'

r Moyie e iv Springs R ie y o

2 95

48° 42'

Ambush Rock Bonners Ferry

48° 40'

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 0 1 2 MILES 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 1 2 KILOMETERS EXPLANATION Canada Survey locations USA P e R n K a d i o b O o m r Map t u e e l i n l area a o l i R e C

Cl ar Montana k Fo S r po k kane R Idaho Washington Sai nt Joe R

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

tac12-0746_fig05 Methods 9

Methods survey lines was between 75 and 100 percent. However, areas of missing data referred to as holidays occurred within The bathymetric data were collected using a multibeam the dataset due to the filtering of macrophytes, editing of echosounder (MBE) system mounted on a USGS-owned and erroneous data points, and areas where it was too shallow to operated 25-foot jet boat research vessel. The echosounding allow complete coverage. component was a 240 kHz ODOM ES3 multibeam echosounder capable of projecting 120, 240, or 480 beams Quality Assurance and Quality Control spanning a max of 120° swath (width of coverage). Figures 6 and 7 show examples of how the multibeam echosounder Quality assurance (QA) and quality control (QC) are collects the corrected elevation point coverage across the critical with MBE surveys to maintain the highest degree of survey swath. For the surveys on the Kootenai, 240 beams accuracy. Qualitative notes documenting anything that might were selected and the port and starboard angles were limited affect the quality of the data, such as wave action, macrophyte to 50° per side for a total angular coverage of 100°. growth, poor GPS quality, and any other observation that A Teledyne TSS DMS-10 dynamic motion reference could degrade the bathymetric data were recorded in the daily unit accounted for heave, pitch, and roll of the vessel. Two field log. 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 Quality Assurance spatial change in the surface speed of underwater sound. The Prior to and during the survey, unique tasks were second velocimeter was used to acquire a depth profile that conducted at specified intervals to prepare the MBE system recorded how the speed of underwater sound varied by depth. for bathymetric surveying, but also to describe the total A Trimble® R8 GPS receiver mounted over the MBE was estimated error within the system. Tasks and descriptions are radio linked to another GPS receiver set over a survey control shown in table 1 for the recommended measurement interval point on land to provide real-time horizontal and vertical for each project and were developed based on requirements positioning. A Hemisphere® VS111 dual-GPS system was from U.S. Army Corps of Engineers (2004), National Oceanic used for the heading and to output a 1 pulse per second (1PPS) and Atmospheric Administration (2011), and system specific output. The entire MBE system is shown in figures 7 and 8. requirements. The order of tasks shown in table 1 is important An ODOM® Real-Time Appliance (RTA) was used because each task is dependent on the preceding task. Quality- to time stamp the MBE, motion reference unit, real-time assurance elements were developed following the input velocimeter, RTK-GPS positioning and elevation, and precise requirements of the Total Propagated Uncertainty (TPU) heading data to within 1 millisecond based on the 1PPS feature built into HYPACK® software. The TPU required a signal from the Hemisphere® VS111. The RTA output the description of the general, environmental, and sensor settings bathymetric data to two laptops, one for data acquisition to best estimate the total error potential in the survey data. and one for data processing. In addition, a Hummingbird® A table of the procedures used for this survey is provided in side‑scan was used for qualitative purposes to verify and note appendixes B and C. unique features (trees, sunken cars, sand dunes, clay steps and Perhaps the most significant quality-assurance element is benches) to the channel bathymetry. A daily field log of the the patch test (table 1). A patch test included running a series bathymetric surveys was kept to record the equipment used, of MBE survey lines to compensate for physical mounting crew members, referenced survey bench marks, sound velocity differences including latency, pitch, roll, and yaw (fig. 10). profiles, file names, and other ancillary information. An Two patch tests were conducted before and after the surveys example of the daily log is provided in appendix A. Figure 9 to ensure the MBE system was correctly offset and calibrated shows an image of each of these components. (appendixes D and E). A complete description of the patch The bathymetric data were collected in the field using test process can be found in U.S. Army Corps of Engineers the HYPACK® software HYSWEEP®. The raw data were (2004) and National Oceanic and Atmospheric Administration then edited using HYPACK®’s MBMAX software. All raw (2011). The offsets from the patch test were applied to the data were initially filtered to exclude the outer 10° of the system prior to the surveys on the Kootenai River. A second multibeam swath. These data were out of tolerance (see patch test was conducted after the Kootenai River bathymetric section, “Quality Assurance”) and therefore excluded from the surveys to ensure the system was still properly aligned and no final data. The edited data were reduced to a 3×3-foot cell size adjustments to the offset coefficients were necessary. Neither as XYZ ASCII data using HYPACK® Combined Uncertainty of the patch tests were completed on the Kootenai River, due and Bathymetric Estimator (CUBE). Two hundred and forty to the poor channel geometry and river currents that are not beams were used for the survey and overlap of adjacent appropriate for a patch test. 10 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

0.0

50°

100° Depth (D)

10.0

NADIR

Swath ≈2*tan(50)*D

20.0 -20.0 0.0 20.0

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

tac12-0746_fig06 Methods 11

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.

tac12-0746_fig07 12 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Multibeam echosounder Velocimeter

Motion reference unit (hidden from view)

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

tac12-0746_fig08 Methods 13

RTK-GPS controller

Hummingbird® side-scan

Data processing PC Data aquisition PC

Daily field log Hemisphere® VS111 dual-GPS receiver ODOM® Real-Time Appliance

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

tac12-0746_fig10 14 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011 verification of these , spatial tide prediction A . Quality Assurance .” Quality Summary measurements should occur at the beginning of each project. probe should be verified that the sound velocity values match factory-calibration values. survey speed should take the following into consideration, 1.survey depths, 2.river currents. Slower 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. the style of survey. Survey. a rectangular surface that is lowered known depth and running the bar check utility within HYSWEEP and depth calculation to In addition, a manual check should be made using the GPS, vertical antenna offsett, verify the estimated corrected depth of MBES. the outcome of control limitations have been established prior to the patch test as they could affect and H/V After each project, a follow-up patch test should occur in the same location using lines to verify test. the first patch test to ensure no changes were incurred during project. If any physical or equipment are made during the project, a new patch test should be surveyed to account for any potential changes this might have to the system. The horizontal position (X,Y) and vertical elevation (Z) verification can be completed multibeam system. to verify an existing or established benchmark in the study area. using the RTK-GPS The frequency of the velocity casts should be third cast should be taken at the end of day. A through the day. increased in areas with a significant stratification. Each of the velocity casts should be loaded into editing file so that changed to the velocity profile is accounted for during survey This will be decided by the results of performance test in section, “ uncertainty, sound speed sensor uncertainty (real-time, cast, spatial-temporal variation, thickness of spatial- uncertainty, profile). uncertainty beyond profile, and max depth of SV temporal layer, and multibeam echosounder) should be measured each time a component is installed. horizontal control within the survey area. If necessary, allow 3 weeks to precise ephemeris results for horizontal control within the survey area. If necessary, The accuracy for the horizontal and static surveys in areas with no existing horizontal and/or vertical control. vertical control order should be clearly stated as well the coordinate system used (State Plane preferred, then UTM). and bandwidth. Each of these should be noted from the manufacturer. angle, frequency, swell, forward-aft seafloor slope, port-starboard water level uncertainty Each echosounder is required to be factory-calibrated once per year. Prior to each project, sound velocity Each echosounder is required to be factory-calibrated once per year. The proper qualitative estimate for a proper survey speed should be considered prior to the start of each survey. A Overlapping requirements (percent coverage) should be decided prior to the start of project and is a function This can be verified using bar check should occur once per project to verify the NADIR depth of multibeam. A patch test should be surveyed prior to the start of each project. It is important that sound velocity calibration A The horizontal position and vertical elevation verification should occur daily to explain the spatial accuracy of second cast should be taken approximately half-way A velocity cast should occur prior to the survey each day. A Beam width restrictions (°) may be required in deeper water where the quality of outer beams exceed . The physical offsets (Foreword, starboard, and vertical) for each of the MBES components (RTK-GPS, MRU, (Foreword, starboard, and vertical) for each of the MBES components (RTK-GPS, The physical offsets Prior to the start of the survey, a reconnaissance survey should occur to verify and/or establish proper vertical and Prior to the start of survey, Angular Coverage, ping rate, beam width, pulse length, steering The general settings include but are not limited to general estimate for the following should be approximated prior to each project: speed of sound, peak-to-peak A precision Measurement ±1 foot per second ± 1 knot (degrees) Varies (%) Varies ± 0.05 foot Varies ± 0.01 foot ± 0.01 foot Varies 3rd order or better Varies Varies interval 1 / project 1 / project 1 / project 1 / project 1 / project 2 / project 1 / day 2–3 / day 1 / project 1 / project 1 / project 1 / project Recommended Task Project quality assurance and control elements for multibeam bathymetric surveys.

calibration limitations verification check measurements and uncertainty estimates and vertical control general settings Sound velocity probe survey speed limitation Vessel Multibeam beam-width Overlapping requirement Bar check verification Patch test Horizontal and vertical casts Velocity Table 1. Table MBES sensor offset MBES sensor offset RTK-GPS horizontal RTK-GPS Multibeam echosounder Environmental settings Methods 15

EXPLANATION

Corrected bed elevation, CA.HSX in feet 2,083 CC.HSX Actual surveyed lines CB.HSX 2,080 C Planned lines C C.HSX CC.HSX CD.HSX

2,070 CE.HSX

Roll test lines

2,060

Pitch lines

2,050 Yaw lines AA.HSX

AE.HSX

BA.HSX

2,040 AF.HSX

B.HSX A.HSX

A B 2,030 AD.HSX

AC.HSX

2,020

Latency lines 2,012

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 0 100 200 300 400 500 FEET 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 50 100 150 METERS

Canada USA P e R n K a d i o b O o m r t u e e l i n l a o l i R e C

Cl ar Montana k Fo S r po k kane R Idaho Washington Map area Sai nt Joe R

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

tac12-0746_fig11 16 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Quality Control was not a suitable location within the Kootenai River for the performance test. The output from the performance test Following the adjustments from the patch test, a includes a summary of how the accuracy of the X,Y, and Z performance test (also referred to as a beam angle check) data are distributed through the swath of the MBE. Typically, provided quality control by quantifying the accuracy of the integrity of the data is diminished as it deviates from the the MBE (fig. 11). The performance test compared a set of center (NADIR) beam. The results of the performance test standard survey data against a known reference surface. The were compared with the minimum performance standards reference surface was created by surveying 10 lines (5 parallel as defined by U.S. Army Corps of Engineers (2004) and are and 5 perpendicular) spaced equal to the depth creating shown in appendix F. 200 percent overlap and edited to remove any data outside of An additional output option from the HYPACK® CUBE 45° from the NADIR beam. The final reference surface is the module used for quality control is the estimated uncertainty. best representative surface for a baseline measure to check the The uncertainty was estimated for each of the estimated performance of the system. Two standard survey lines were gridded surfaces, for this study a 3×3-foot grid (table 2). Each surveyed across the center of the reference surface to be used estimated grid elevation was estimated based on the most as the performance measure. The standard survey lines were statistically significant elevation within the grid. The total edited using the same methods applied to all data collected. number of data points used to develop the grid output were The performance test for the Kootenai River bathymetric highly variable and depended on the distance from NADIR surveys was conducted on April 28, 2011, at Lake Coeur (decreasing density from NADIR), depth of water (decreasing d’Alene, Idaho. It was recommended that the performance density with increasing depth), and amount of overlapping test be done on the same body of water as the study, but there 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]

Data-quality objectives (±) ft Quality-control results (±) ft Multibeam Substrate Braided reach Performance Other echosounder Enhancement Hard Soft cross-section standard surveys bathymetric Project near bottom bottom monitoring and studies survey in Shorty’s Island and surveys meander reach Myrtle Creek 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 < 6 6.0 16.0 <1 <1 <1 Accuracy (ft) 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

EXPLANATION Depth of water, in feet 2,083 001_0814.HSX 2,080

2,070

002_0816.HSX

2,060

E.HSX D.HSX

CF.HSX

CG.HSX

BB.HSX AG.HSX

2,050 003_0818.HSX 003_0827.HSX

2,040

004_0820.HSX

2,030

2,020 005_0823.HSX AH.HSX

2,012

Base from U.S. Geological Survey digital data, 1:100,000, 1980, and NAIP 2011 1-meter 0 100 200 300 400 FEET 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 50 100 METERS EXPLANATION Planned lines Canada USA 004_0820.HSX P Raw lines e R n K a d i o b O o m r t u e e l i n l a o l i R e C

Cl ar Montana k Fo S r po k kane R Idaho Washington Map area Sai nt Joe R

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

tac12-0746_fig11 18 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Bathymetric Survey Table 3. Multibeam echosounder bathymetric survey in meander reach.

Data [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] Edited raw data are presented in a generic ASCII XYZ format in Survey Survey File Image the most raw form so that it can be extent date name used in various types of geospatial River Mile 151 05-19-2011 RM151.xyz 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 River Mile 150 05-19-2011 RM150.xyz description and ASCII XYZ data are provided in the metadata for each survey area.

Multibeam Echosounding Survey in Meander Reach River Mile 149 05-12-2011 RM149.xyz

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 River Mile 141 05-3-2011 RM141.xyz desirable as multibeam echosounder (MBE) bathymetry for use in two- dimensional 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 River Mile 140 05-3-2011 RM140.xyz 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. Bathymetric Survey Data 19

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]

Survey Survey File Image extent date name River Mile 139 05-04-2011 to RM139.xyz 05-05-2011

River Mile 138 05-5-2011 RM138.xyz 20 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

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]

Survey Survey File Image extent date name River Mile 137 05-31-2011 RM137.xyz

River Mile 136 06-1-2011 RM136.xyz Bathymetric Survey Data 21

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]

Survey Survey File Image extent date name River Mile 135 06-01-2011 to RM135.xyz 06-02-2011

River Mile 134 06-2-2011 RM134.xyz 22 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 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.

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 Survey Link to map image File name extent date 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 Substrate_Enhancement_Project_ 07-13-2011 bathymetry_July_2011 Bathymetric Survey Data 23

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.

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 Survey Lind to map image File name extent date Braided reach 05-16-2011 to KR2011_BraidedXSections_May.xyz cross sections 05-17-2011

07-12-2011 KR2011_BraidedXSections_July.xyz 24 Bathymetric Surveys of the Kootenai River near Bonners Ferry, Idaho—Water Year 2011

Acknowledgments National Oceanic and Atmospheric Administration, 2011, 2011 Field procedure manual: National Oceanic and Atmospheric The author expresses appreciation to the Kootenai Administration, 333 p., accessed April 27, 2012, at http:// Tribe of Idaho and to the Bonneville Power Administration www.nauticalcharts.noaa.gov/hsd/fpm/fpm.htm. for funding and logistical support during the bathymetric Paragamian, V.L., Kruse, Gretchen, and Wakkinen, Virginia, surveys. The author also would like to thank all USGS Idaho 2001, Spawning habitat of Kootenai River white sturgeon, Water Science Center colleagues for their assistance with post-Libby Dam: North American Journal of Fisheries data collection. 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 References Cited sturgeon: Journal of Applied Ichthyology, v. 18, p. 608–616.

Barton G.J., Moran E.H., and Berenbrock, C., 2004, Surveying Partridge, F., 1983, Kootenai River fisheries investigations: cross sections of the Kootenai River between Libby Dam, Boise, Idaho Department of Fish and Game, Job Montana, and Kootenay Lake, British Columbia, Canada: Completion Report, Project F-73-R-5, Subproject IV, U.S. Geological Survey Open-File Report 2004–1045, Study IV. 35 p., accessed August 3, 2012, at http://id.water.usgs.gov/ Redwing Naturalists, 1996, History of diking on the Kootenay PDF/ofr041045/. River floodplain in British Columbia: Report of Redwing Boundary County Historical Society, 1987, The history Naturalists to Habitat Enhancement Branch, Department of of Boundary County, Idaho: Portland, Oregon, Taylor Fisheries and Oceans, British Columbia, Canada, p. 17–14, Publishing Company, p. 43–46 and 48. and 20–22. Federal Register, 1994, Endangered and threatened wildlife Turney-High, H.H., 1969, Ethnography of the Kutenai: New and plants—Determination of endangered status for the York, Kraus Reprint Company, p. 44. Kootenai River population of the white sturgeon: Federal U.S. Army Corps of Engineers, 2004, Engineering and Design, Register, v. 59, no. 171, p. 45,989-46,002, accessed Hydrographic surveying, EM 1110-2-1003, Change 1: April 27, 2012, at http://ecos.fws.gov/docs/federal_register/ Washington, DC, U.S. Army Corps of Engineers, accessed fr2678.pdf. August 3, 2012, at http://140.194.76.129/publications/eng- Federal Register, 2008, Endangered and threatened wildlife manuals/EM_1110-2-1003_pfl/toc.htm. and plants—Critical habitat revised designation for U.S. Fish and Wildlife Service, 1999, Recovery plan for the Kootenai River population of the white sturgeon the white sturgeon (Acipenser transmontanus): Kootenai (Acipenser transmontanus): Federal Register, v. 73, no. 132, River population: U.S. Fish and Wildlife Service, Portland, p. 39,505–39,523, accessed April 27, 2012, at http:// Oregon, 96 p. plus appendixes, accessed April 27, 2012, at www.gpo.gov/fdsys/pkg/FR-2008-07-09/pdf/E8-15134. http://ecos.fws.gov/docs/recovery_plan/990930b.pdf. pdf#page=1. U.S. Fish and Wildlife Service, 2006, Fish and Wildlife Kock, T.J., Congleton, J.L., and Anders, P.J., 2006, Effects Service biological opinion regarding the effects of Libby of sediment cover on survival and development of white Dam operations on the Kootenai River white sturgeon, sturgeon embryos: North American Journal of Fisheries bull trout, and Kootenai sturgeon critical habitat: Fish and Management, v. 26, no. 1, p. 134–141. Wildlife Service Biological Opinion, 1-9-01-F-0279R, Kootenai Tribe of Idaho, 2009, Kootenai River Habitat 153 p. Restoration Project Master Plan: Kootenai Tribe of Idaho, 291 p., accessed April 27, 2012, at http://www.kootenai.org/ fish_restoration.html. 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 Director, Idaho Water Science Center U.S. Geological Survey 230 Collins Road 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