The Kootenai River white sturgeon (Acipenser transmontanus) and other native fish species are culturally important to the Kootenai Tribe of Idaho, but their habitat and recruitment have been affected by anthropogenic changes to the river. Although the interconnections among anthropogenic changes and their impacts on fish are complex, the Kootenai Tribe of Idaho, in cooperation with other agencies, has been trying to understand and promote native fish recruitment through the development and implementation of the Kootenai River Habitat Restoration Program. As part of this effort, the U.S. Geological Survey collected sediment and streamflow information and evaluated use of acoustic backscatter as a sediment surrogate for estimating continuous suspended-sediment concentration at three sites in the Kootenai River white sturgeon critical habitat during water years 2011–14.

During the study, total suspended-sediment and fines concentrations were driven primarily by contributions from tributaries flowing into the Kootenai River between Libby Dam and the study area and were highest during rain-on-snow events in those tributary watersheds. On average, the relative percentage of suspended-sediment concentration in equal-width-increment samples collected in water years 2011–14 composed of fines less than 0.0625 mm (called washload) was 73, 71, and 70 percent at the Below Moyie, Crossport, and Tribal Hatchery sites, respectively. Suspended sand transport often increased with high streamflows, typically but not always associated with releases from Libby Dam. Bedload measured at the Crossport site was about 5 percent, on average, of the total sediment load measured in samples collected in water years 2011–13 and was positively correlated with suspended-sediment load. Comparisons with regional regression and envelope lines for suspended-sediment and bedload transport in relation to unregulated drainage area (drainage area downstream of Libby Dam) show that sediment transport was substantially less in the Kootenai River than in selected, minimally regulated Rocky Mountain rivers.

Acoustic surrogate ratings were developed between backscatter data collected using acoustic Doppler velocity meters (ADVMs) and results of suspended-sediment samples. Ratings were successfully fit to various sediment size classes (total, fines, and sands) using ADVMs of different frequencies (1.5 and 3 megahertz). Surrogate ratings also were developed using variations of streamflow and seasonal explanatory variables. The streamflow surrogate ratings produced average annual sediment load estimates that were 8–32 percent higher, depending on site and sediment type, than estimates produced using the acoustic surrogate ratings. The streamflow surrogate ratings tended to overestimate suspended-sediment concentrations and loads during periods of elevated releases from Libby Dam as well as on the falling limb of the streamflow hydrograph. Estimates from the acoustic surrogate ratings more closely matched suspended-sediment sample results than did estimates from the streamflow surrogate ratings during these periods as well as for rating validation samples collected in water year 2014. Acoustic surrogate technologies are an effective means to obtain continuous, accurate estimates of suspended-sediment concentrations and loads for general monitoring and sediment-transport modeling. In the Kootenai River, continued operation of the acoustic surrogate sites and use of the acoustic surrogate ratings to calculate continuous suspended-sediment concentrations and loads will allow for tracking changes in sediment transport over time.