Introduction

Anthropogenic influence to the Kootenai River (or Kootenay for the Canadian areas) is evident upstream of, in, 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 29.5 km reach extending from RKM 257.0, downstream of the Moyie River, downstream to RKM 228.0 in the meander reach downstream of Shorty’s Island. This critical habitat was recently extended 11.4 km upstream to include the braided reach from RKM 246.0 to 257.0 (Federal Register, 2008).

Historical references indicate that dikes were built on natural levees early in the 20th century to protect agriculture from flooding on the Kootenai River floodplain (Turney-High,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, significantly altered the 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 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 declining 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 declining 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 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. 39513 and 39522). The study of sediment transport in the federally designated critical habitat of the Kootenai River white sturgeon is crucial to meeting this objective.

Efforts to mitigate and alter the effect of the anthropogenic activity in the white sturgeon critical habitat are being investigated by Federal, State, and Tribal scientists, as well as private organizations and International agencies. Between December 2007 and June 2008, the U.S. Geological Survey (USGS) conducted suspended- and bedload-sediment sampling on the Kootenai River. Suspended sediment refers to the sediment that remains in suspension as it moves downstream. The suspended material generally is uniformly distributed through the water column, and it moves downstream at a rate relative to the water velocity (Edwards and Glysson, 1999). “Bedload sediment is the sediment that is moved by saltation, rolling, or sliding on or near the streambed, essentially in continuous contact with it” (Osterkamp, 2008).

Three sampling sites were selected to represent the different hydrologic conditions in the white sturgeon critical habitat. Samples were collected during specific flow conditions. The suspended- and bedload-sediment samples were then analyzed and total sediment loading estimates were prepared.

Purpose and Scope

This report presents and discusses the sediment-transport characteristics of the white sturgeon critical habitat in the Kootenai River near Bonners Ferry, Idaho, to support the development of sediment transport models and the assessment of feasibility of habitat assessment. (U.S. Fish and Wildlife Service, 2006).

The scope of this report is limited to sediment transport in the USFWS-designated critical habitat of the Kootenai River population of white sturgeon outlined in the Federal Register (2008).

River kilometer designators in this report are based on those presented in the Federal Register final ruling of 2008 (Federal Register, 2008). Berenbrock (2006, p. 4) outlines how these designators were developed and how they differ from other published values from other agencies.

Description of Study Area

The Kootenai River is the second largest drainage in terms of discharge volume in the Columbia River basin. From its headwaters in the Rocky, Salish, and Purcell Mountain ranges, the Kootenai River flows to the south through northwestern Montana. Continuing southwest 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 Mountain range (fig. 1). In 1972, Libby Dam was constructed on the upper Kootenai River near Libby, Montana, creating Lake Koocanusa, a 145-km long reservoir with a full-pool storage capacity of 7,262.37 hm³ (U.S. Fish and Wildlife Service, 2006).

The major tributary systems feeding the Kootenai River downstream of Libby Dam are the Fisher and Yaak Rivers in Montana, and the Moyie River in Idaho. The Fisher River has a drainage area of about 2,160 km² at its confluence with the Kootenai River at RKM 351.2. Based on 40 years of USGS streamflow data for the Fisher River near Libby Montana (12302055), an estimated bankfull discharge (66.7 percent exceedance probability) is about 62 m³/s (2,187 ft³/s) (appendix A). The Yaak River has a drainage area of about 1,984 km² at its confluence with the Kootenai River at RKM 285.9. Based on 54 years of USGS streamflow data for the Yaak River near Libby Montana (12302055), a discharge estimate for bankfull conditions (66.7 percent exceedance probability) is about 153 m³/s (5,391 ft³/s) (appendix A). The Moyie River is controlled by Moyie Dam 2.59 km upstream of the confluence from the Kootenai River. A frequency analysis was not applied to this drainage, because it is a regulated system with an unnatural runoff pattern.

The study reach of the Kootenai River includes three major geomorphic reaches: the canyon, braided, and meander reaches (fig. 2). The canyon reach begins near Kootenai Falls (RKM 312.0) (fig. 1) and continues downstream to near the confluence of the Moyie River (RKM 257.0). The braided reach extends from the end of the canyon reach downstream to Bonners Ferry (RKM 246.0). The meander reach extends from the braided reach downstream to the confluence with Kootenay Lake in British Columbia (RKM 120.0) (fig. 1). The most upstream part of the meander reach includes a 1.5 km reach referred to as the “transition zone” that joins the braided and meander reaches between RKMs 245.9 and 244.5 (Federal Register, 2008). The transition zone refers to the location of the transition between backwater from Kootenay Lake and free-flowing river. This transition often occurs between RKMs 244.6 and 252.7 with an average location at RKM 247.8 (Berenbrock, 2005).

Previous Investigations

An extensive sediment data record for the Kootenai River in the State of Idaho is available, and a complete listing of these data can be accessed through the USGS National Water Information System (NWIS) web site at http://nwis.waterdata.usgs.gov/id/nwis/qwdata. A list of sampling sites on the Kootenai River for which sediment data are available is shown in table 1.

The sediment data can be used to provide insight into the geomorphic and hydrologic changes to the Kootenai River before and after the construction of Libby Dam (Barton, 2004; Berenbrock, 2005).