A study was conducted to identify habitat characteristics associated with age 0+ White Sturgeon (Acipenser transmontanus Richardson, 1863) recruitment in three reaches of the Columbia River Basin: Skamania reach (consistent recruitment), John Day reach (intermittent/inconsistent recruitment), and Kootenai reach (no recruitment). Our modeling approach involved numerous steps. First, we collected information about substrate, embeddedness, and hydrodynamics in each reach. Second, we developed a set of spatially explicit predictor variables. Third, we built two habitat (probability) models with Skamania reach training data where White Sturgeon recruitment was consistent. Fourth, we created spawning maps of each reach by populating the habitat models with in-reach physical metrics (substrate, embeddedness, and hydrodynamics). Fifth, we examined model accuracy by overlaying spawning locations in Skamania and Kootenai reaches with habitat predictions obtained from probability models. Sixth, we simulated how predicted habitat changed in each reach after manipulating physical conditions to more closely match Skamania reach. Model verification confirmed White Sturgeon generally spawned in locations with higher model probabilities in Skamania and Kootenai reaches, indicating the utility of extrapolating the models. Model simulations revealed significant gains in White Sturgeon habitat in all reaches when spring flow increased, gravel/cobble composition increased, or embeddedness decreased. The habitat models appear well suited to assist managers when identifying reach-specific factors limiting White Sturgeon recruitment in the Columbia River Basin or throughout its range.

Condit Dam is one of the largest hydroelectric dams ever removed in the USA. Breached in a single explosive event in October 2011, hundreds-of-thousands of cubic metres of sediment washed down the White Salmon River onto spawning grounds of a threatened species, Columbia River tule fall Chinook salmon Oncorhynchus tshawytscha. We investigated over a 3-year period (2010-2012) how dam breaching affected channel morphology, river hydraulics, sediment composition and tule fall Chinook salmon (hereafter tule salmon') spawning habitat in the lower 1.7km of the White Salmon River (project area). As expected, dam breaching dramatically affected channel morphology and spawning habitat due to a large load of sediment released from Northwestern Lake. Forty-two per cent of the project area that was previously covered in water was converted into islands or new shoreline, while a large pool near the mouth filled with sediments and a delta formed at the mouth. A two-dimensional hydrodynamic model revealed that pool area decreased 68.7% in the project area, while glides and riffles increased 659% and 530%, respectively. A spatially explicit habitat model found the mean probability of spawning habitat increased 46.2% after dam breaching due to an increase in glides and riffles. Shifting channels and bank instability continue to negatively affect some spawning habitat as sediments continue to wash downstream from former Northwestern Lake, but 300m of new spawning habitat (river kilometre 0.6 to 0.9) that formed immediately post-breach has persisted into 2015. Less than 10% of tule salmon have spawned upstream of the former dam site to date, but the run sizes appear healthy and stable. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Kokanee salmon (Oncorhynchus nerka) are a keystone species in Lake Pend Oreille in northern Idaho, historically supporting a high-yield recreational fishery and serving as the primary prey for the threatened native bull trout (Salvelinus confluentus) and the Gerrard-strain rainbow trout (Oncorhynchus mykiss). After 1965, the kokanee population rapidly declined and has remained at a low level of abundance. Lake Pend Oreille is one of the deepest lakes in the United States, the largest lake in Idaho, and home to the U.S. Navy Acoustic Research Detachment Base. The U.S. Geological Survey and Idaho Department of Fish and Game are mapping the bathymetry, morphology, and the lakebed geologic units and embeddedness of potential kokanee salmon spawning habitat in Lake Pend Oreille. Relations between lake morphology, lakebed geologic units, and substrate embeddedness are characterized for the shore zone, rise zone, and open water in bays and the main stem of the lake. This detailed knowledge of physical habitat along the shoreline of Lake Pend Oreille is necessary to better evaluate and develop kokanee recovery actions.

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River channel construction projects aimed at restoring or improving degraded waterways have become common but have been variously successful. In this report a methodology is proposed to evaluate channel designs before channels are built by using multidimensional modeling and analysis. This approach allows detailed analysis of water-surface profiles, sediment transport, and aquatic habitat that may result if the design is implemented. The method presented here addresses the need to model a range of potential stream-discharge and channel-roughness conditions to best assess the function of the design channel for a suite of possible conditions. This methodology is demonstrated by using a preliminary channel-restoration design proposed for a part of the Kootenai River in northern Idaho designated as critical habitat for the endangered white sturgeon (Acipenser transmontanus) and evaluating the design on the basis of simulations with the Flow and Sediment Transport with Morphologic Evolution of Channels (FaSTMECH) model. This evaluation indicated substantial problems with the preliminary design because boundary conditions used in the design were inconsistent with best estimates of future conditions. As a result, simulated water-surface levels did not meet target levels that corresponded to the designed bankfull surfaces; therefore, the flood plain would not function as intended. Sediment-transport analyses indicated that both the current channel of the Kootenai River and the design channel are largely unable to move the bed material through the reach at bankfull discharge. Therefore, sediment delivered to the design channel would likely be deposited within the reach instead of passing through it as planned. Consequently, the design channel geometry would adjust through time. Despite these issues, the design channel would provide more aquatic habitat suitable for spawning white sturgeon (Acipenser transmontanus) at lower discharges than is currently available in the Kootenai River. The evaluation methodology identified potential problems with the design channel that can be addressed through design modifications to better meet project objectives before channel construction.

The Kootenai Tribe of Idaho, in cooperation with local, State, Federal, and Canadian agency co-managers and scientists, is assessing the feasibility of a Kootenai River habitat restoration project in Boundary County, Idaho. The restoration project is focused on recovery of the endangered Kootenai River white sturgeon (Acipenser transmontanus) population, and simultaneously targets habitat-based recovery of other native river biota. River restoration is a complex undertaking that requires a thorough understanding of the river and floodplain landscape prior to restoration efforts. To assist in evaluating the feasibility of this endeavor, the U.S. Geological Survey developed an updated one-dimensional hydraulic model of the Kootenai River in Idaho between river miles (RMs) 105.6 and 171.9 to characterize the current hydraulic conditions. A previously calibrated model of the study area, based on channel geometry data collected during 2002 and 2003, was the basis for this updated model. New high-resolution bathymetric surveys conducted in the study reach between RMs 138 and 161.4 provided additional detail of channel morphology. A light detection and ranging (LIDAR) survey was flown in the Kootenai River valley in 2005 between RMs 105.6 and 159.5 to characterize the floodplain topography. Six temporary gaging stations installed in 2006-08 between RMs 154.1 and 161.2, combined with five permanent gaging stations in the study reach, provided discharge and water-surface elevations for model calibration and verification. Measured discharges ranging from about 4,800 to 63,000 cubic feet per second (ft3/s) were simulated for calibration events, and calibrated water-surface elevations ranged from about 1,745 to 1,820 feet (ft) throughout the extent of the model. Calibration was considered acceptable when the simulated and measured water-surface elevations at gaging stations differed by less than (+/-)0.15 ft. Model verification consisted of simulating 10 additional events with measured discharges ranging from about 4,900 to 52,000 ft3/s, and comparing simulated and measured water-surface elevations at gaging stations. Average water-surface-elevation error in the verification simulations was 0.05 ft, with the error ranging from -1.17 to 0.94 ft over the range of events and gaging stations. Additional verification included a graphical comparison of measured average velocities that range from 1.0 to 6.2 feet per second to simulated velocities at four sites within the study reach for measured discharges ranging from about 7,400 to 46,600 ft3/s. The availability of high-resolution bathymetric and LIDAR data, along with the additional gaging stations in the study reach, allowed for more detail to be added to the model and a more thorough calibration, sensitivity, and verification analysis to be conducted. Model resolution and performance is most improved between RMs 140 and 160, which includes the 18.3-mile reach of the Kootenai River white sturgeon critical habitat.

Figure 1. Site map and location of Marcus flats and China Bend study reaches. Shaded relief from U.S. Geological Survey Landsat Tri-decadal State satellite Mosaic Washington, 2001, available from the USGS Store at http://usgs.store.gov/. Lake Roosevelt National Recreation Area boundary accessed on Dec. 16, 2010 at http://www.nps.gov/carto/PDF/LAROmap1.pdf. Colville National Forest boundary from the U.S. Dept. of Agriculture National Forest Service accessed on Dec. 16, 2010 at http://www.fs.fed.us/r6/datalibrary/gis/colville/index.shtml, Okanogan National Forest Service boundary at http://www.fs.fed.us/r6/data-library/gis/okanogan/index.shtml, Little Pend Oreille National Wildlife Refuge boundary from http://www.fws.gov/littlependoreille/pdf/PublicUseRefugeMap.pdf. Spokane Indian Reservation boundary accessed on Dec. 16, 2010 at http://www.spokanetribe.com/reservation. Colville Indian Reservation Boundary from http://www.colvilletribes.com/map%20of%20non%20tribe%20camp.html. River miles from National Oceanic and Atmospheric Administration (NOAA), Office of Coast Survey at http://www.nauticalcharts.noaa.gov/. All boundaries are generalized and approximately located and for display purposes only. Inholdings have not been shown. RM 725

Kootenai River white sturgeon spawn in an 18-km reach of the Kootenai River, Id. Since completion of Libby Dam upstream from the spawning reach in 1972, 1974 is the only year with documented significant recruitment of juvenile fish. Where successful in other rivers, white sturgeon spawn over clean coarse material of gravel size or larger. The channel substrate in the current (2008) 18-km spawning reach is composed primarily of sand and some buried gravel; within a few kilometers upstream there is an extended reach of clean gravel, cobble, and bedrock. We used a quasi-three-dimensional flow and sediment-transport model along with the locations of collected sturgeon eggs as a proxy for spawning location from 1994 to 2002 to gain insight into spawning-habitat selection in a reach which is currently unsuitable due to the lack of coarse substrate. Spatial correlations between spawning locations and simulated velocity and depth indicate fish select regions of higher velocity and greater depth within any river cross section to spawn. These regions of high velocity and depth occur in the same locations regardless of the discharge magnitude as modeled over a range of pre- and postdam flow conditions. A flow and sediment-transport simulation shows high discharge, and relatively long-duration flow associated with predam flow events is sufficient to scour the fine sediment overburden, periodically exposing existing lenses of gravel and cobble as lag deposits in the current spawning reach. This is corroborated by video observations of bed surface material following a significant flood event in 2006, which show gravel and cobble present in many locations in the current spawning reach. Thus, both modeling and observations suggest that the relative rarity of extremely high flows in the current regulated flow regime is at least partly responsible for the lack of successful spawning; in the predam flow regime, frequent high flows removed the fine sediment overburden, unveiling coarse material and providing suitable substrate in the current spawning reach.

During 2005, the U.S. Geological Survey (USGS) developed, calibrated, and validated a multidimensional flow model for simulating streamflow in the white sturgeon spawning habitat of the Kootenai River in Idaho. The model was developed as a tool to aid understanding of the physical factors affecting quality and quantity of spawning and rearing habitat used by the endangered white sturgeon (Acipenser transmontanus) and for assessing the feasibility of various habitat-enhancement scenarios to re-establish recruitment of white sturgeon. At the request of the Kootenai Tribe of Idaho, the USGS extended the two-dimensional flow model developed in 2005 into a braided reach upstream of the current white sturgeon spawning reach. Many scientists consider the braided reach a suitable substrate with adequate streamflow velocities for re-establishing recruitment of white sturgeon. The 2005 model was extended upstream to help assess the feasibility of various strategies to encourage white sturgeon to spawn in the reach. At the request of the Idaho Department of Fish and Game, the USGS also extended the two-dimensional flow model several kilometers downstream of the white sturgeon spawning reach. This modified model can quantify the physical characteristics of a reach that white sturgeon pass through as they swim upstream from Kootenay Lake to the spawning reach. The USGS Multi-Dimensional Surface-Water Modeling System was used for the 2005 modeling effort and for this subsequent modeling effort. This report describes the model applications and limitations, presents the results of a few simple simulations, and demonstrates how the model can be used to link physical characteristics of streamflow to the location of white sturgeon spawning events during 1994-2001. Model simulations also were used to report on the length and percentage of longitudinal profiles that met the minimum criteria during May and June 2006 and 2007 as stipulated in the U.S. Fish and Wildlife Biological Opinion.

In 1994, the Kootenai River white sturgeon (Acipenser transmontanus) was listed as an Endangered Species as a direct result of two related observations. First, biologists observed that the white sturgeon population in the Kootenai River was declining. Second, they observed a decline in recruitment of juvenile sturgeon beginning in the 1950s with an almost total absence of recruitment since 1974, following the closure of Libby Dam in 1972. This second observation was attributed to changes in spawning and (or) rearing habitat resulting from alterations in the physical habitat, including flow regime, sediment-transport regime, and bed morphology of the river. The Kootenai River White Sturgeon Recovery Team was established to find and implement ways to improve spawning and rearing habitat used by white sturgeon. They identified the need to develop and apply a multidimensional flow model to certain reaches of the river to quantify physical habitat in a spatially distributed manner. The U.S. Geological Survey has addressed these needs by developing, calibrating, and validating a multidimensional flow model used to simulate streamflow and sediment mobility in the white sturgeon critical-habitat reach of the Kootenai River. This report describes the model and limitations, presents the results of a few simple simulations, and demonstrates how the model can be used to link physical characteristics of streamflow to biological or other habitat data. This study was conducted in cooperation with the Kootenai Tribe of Idaho along a 23-kilometer reach of the Kootenai River, including the white sturgeon spawning reach near Bonners Ferry, Idaho that is about 108 to 131 kilometers below Libby Dam. U.S. Geological Survey's MultiDimensional Surface-Water Modeling System was used to construct a flow model for the critical-habitat reach of the Kootenai River white sturgeon, between river kilometers 228.4 and 245.9. Given streamflow, bed roughness, and downstream water-surface elevation, the model computes the velocity field, water-surface elevations, and boundary shear stress throughout the modeled reach. The 17.5 kilometer model reach was subdivided into two segments on the basis of predominant grain size: a straight reach with a sand, gravel, and cobble substrate located between the upstream model boundary at river kilometer 245.9 and the upstream end of Ambush Rock at river kilometer 244.6, and a meandering reach with a predominately sand substrate located between upstream end of Ambush Rock and the downstream model boundary at river kilometer 228.4. Model cell size in the x and y (horizontal) dimensions is 5 meters by 5 meters along the computational grid centerline with 15 nodes in the z (vertical) dimension. The model was calibrated to historical streamflows evenly distributed between 141.6 and 2,548.9 cubic meters per second. The model was validated by comparing simulated velocities with velocities measured at 15 cross sections during steady streamflow. These 15 cross sections were each measured multiple (7-13) times to obtain velocities suitable for comparison to the model results. Comparison of modeled and measured velocities suggests that the model does a good job of reproducing flow patterns in the river, although some discrepancies were noted. The model was used to simulate water-surface elevation, depth, velocity, bed shear stress, and sediment mobility for Kootenai River streamflows of 170, 566, 1,130, 1,700, and 2,270 cubic meters per second (6,000, 20,000, 40,000, 60,000, and 80,000 cubic feet per second). The three lowest streamflow simulations represent a range of typical river conditions before and since the construction of Libby Dam, and the highest streamflow simulation (2,270 cubic meters per second) is approximately equal to the annual median peak streamflow prior to emplacement of Libby Dam in 1972. Streamflow greater than 566 cubic meters per second were incrementally increased by 570 cubic meters per second. For each

In 1994, the Kootenai River white sturgeon (Acipenser transmontanus) was listed as an Endangered Species. In response to the listing, the Kootenai River White Sturgeon Recovery Team was established to find and implement ways to improve spawning and rearing habitat used by white sturgeon. The team identified the need to develop and apply a multidimensional flow model to certain reaches of the river to quantify physical habitat in a spatiallydistributed manner. The U.S. Geological Survey has addressed these needs by using the agency’s MultiDimensional Surface-Water Modeling System (MD_SWMS) to construct a flow model for the critical-habitat reach of the Kootenai River white sturgeon near Bonners Ferry, Idaho. This paper describes the altered white sturgeon habitat and the model, presents the results of a few simple simulations, and demonstrates how the model can be used to link physical characteristics of streamflow to biological or other habitat data. This study was conducted in cooperation with the Kootenai Tribe of Idaho, the Idaho Department of Fish and Game, and the Bonneville Power Authority.

Many local, State, and Federal agencies have concerns over the declining population of white sturgeon (Acipenser transmontanus) in the Kootenai River and the possible effects of the closure and subsequent operation of Libby Dam in 1972. In 1994, the Kootenai River white sturgeon was listed as an Endangered Species. A year-long field study was conducted in cooperation with the Kootenai Tribe of Idaho along a 21.7-kilometer reach of the Kootenai River including the white sturgeon spawning reach near Bonners Ferry, Idaho, approximately 111 to 129 kilometers below Libby Dam. During the field study, data were collected in order to map the channel substrate in the white sturgeon spawning reach. These data include seismic subbottom profiles at 18 cross sections of the river and sediment cores taken at or near the seismic cross sections. The effect that Libby Dam has on the Kootenai River white sturgeon spawning substrate was analyzed in terms of changes in suspended-sediment transport, aggradation and degradation of channel bed, and changes in the particle size of bed material with depth below the riverbed. The annual suspended-sediment load leaving the Kootenai River white sturgeon spawning reach decreased dramatically after the closure of Libby Dam in 1972: mean annual pre-Libby Dam load during 1966–71 was 1,743,900 metric tons, and the dam-era load during 1973–83 was 287,500 metric tons. The amount of sand-size particles in three suspended-sediment samples collected at Copeland, Idaho, 159 kilometers below Libby Dam, during spring and early summer high flows after the closure of Libby Dam is less than in four samples collected during the pre-Libby Dam era. The supply of sand to the spawning reach is currently less due to the reduction of high flows and a loss of 70 percent of the basin after the closure of Libby Dam. The river's reduced capacity to transport sand out of the spawning reach is compensated to an unknown extent by a reduced load of sand entering the spawning reach. Since the closure of Libby Dam, the most notable change in channel geometry at the Copeland streamflow gaging station was the initiation of cyclical aggradation and degradation of the riverbed in the center of the channel. The aggradation and degradation of the riverbed are reflected in a twofold increase, from 1.3 to 2.5 meters, in the fluctuation of the minimum riverbed elevation, which suggests that during the Libby Dam era, parts of the riverbed in the spawning reach may have aggraded or degraded by as much as 2.5 meters. Before the closure of Libby Dam, there was a greater propensity for aggradation and degradation of sand over the discontinuous gravel and cobble layers in the buried gravelcobble reach at Bonners Ferry. The gravel and cobble in this reach, 111.3 to 115.9 kilometers below Libby Dam, are buried by sand. Unregulated spring snowmelt-runoff flows flushed part of the sand layer and exposed some of the buried gravel-cobble layer because streamflow velocities were higher at that time. Unregulated autumn-winter base flows gradually deposited silt and sand and reestablished a sand layer, burying the gravel-cobble layer. This cyclical process of aggradation and degradation of the riverbed sediment is reflected in the alternating gravel-cobble layers and sand layers found in sediment core K18-TH taken as part of this project. White sturgeon spawning substrate in the Kootenai River meander reach is currently composed of alluvial sand that forms sand dunes and of minor amounts of lacustrine clay and silt that generally are found in the river's thalweg. The present substrate composition in the meander reach is considered similar to that which existed prior to closure of Libby Dam, with one possible exception. Prior to closure of Libby Dam, minor amounts of gravel and cobble may have been exposed on the riverbed in the spawning reach just below the mouth of Myrtle Creek 230 kilometers below Libby Dam. The substrate composition near Shorty Island, 234 kilometers below Libby Dam, a notable white sturgeon spawning reach, is predominantly sand and is similar to that which existed prior to closure of Libby Dam.

The State of Idaho and local water users are concerned that streamflow depletion in the Portneuf River in Caribou and Bannock Counties is linked to ground-water withdrawals for irrigated agriculture. A year-long field study during 2001 02 that focused on monitoring surface- and ground-water relations was conducted, in cooperation with the Idaho Department of Water Resources, to address some of the water-user concerns. The study area comprised a 10.2-mile reach of the Portneuf River downstream from the Chesterfield Reservoir in the broad Portneuf Valley (Portneuf River Valley reach) and a 20-mile reach of the Portneuf River in a narrow valley downstream from the Portneuf Valley (Pebble-Topaz reach). During the field study, the surface- and ground-water relations were dynamic. A losing river reach was delineated in the middle of the Portneuf River Valley reach, centered approximately 7.2 miles downstream from Chesterfield Reservoir. Two seepage studies conducted in the Portneuf Valley during regulated high flows showed that the length of the losing river reach increased from 2.6 to nearly 6 miles as the irrigation season progressed.Surface- and ground-water relations in the Portneuf Valley also were characterized from an analysis of specific conductance and temperature measurements. In a gaining reach, stratification of specific conductance and temperature across the channel of the Portneuf River was an indicator of ground water seeping into the river.An evolving method of using heat as a tracer to monitor surface- and ground-water relations was successfully conducted with thermistor arrays at four locations. Heat tracing monitored a gaining reach, where ground water was seeping into the river, and monitored a losing reach, where surface water was seeping down through the riverbed (also referred to as a conveyance loss), at two locations.Conveyance losses in the Portneuf River Valley reach were greatest, about 20 cubic feet per second, during the mid-summer regulated high flows. Conveyance losses in the Pebble-Topaz reach were greatest, about 283 cubic feet per second, during the spring regulated high flows and were attributed to a hydroelectric project.Comparison of water levels in 30 wells in the Portneuf Valley during September and October 1968 and 2001 indicated long-term declines since 1968; the median decline was 3.4 feet. September and October were selected for characterizing long-term ground-water-level fluctuations because declines associated with irrigation reach a maximum at the end of the irrigation season. The average annual snowpack in the study area has declined significantly; 1945 85 average annual snowpack was 16.1 inches, whereas 1986 through 2002 average annual snowpack was 11.6 inches. Water-level declines during 1998 2002 may be partially attributable to the extended dry climatic conditions. It is unclear whether the declines could be partially attributed to increases in ground-water withdrawals. Between 1968 and 1980, water rights for ground-water withdrawals nearly doubled from 23,500 to 46,000 acre-feet per year. During this period, ground-water levels were relatively constant and did not exhibit a declining trend that could be related to increased ground-water withdrawal rights. However, ground-water withdrawals are not measured in the valley; thus, the amount of water pumped is not known. Since the 1990s, there have been several years when the Chesterfield Reservoir has not completely refilled, and the water in storage behind the reservoir has been depleted by the middle of the irrigation season. In this situation, surface-water diversions for irrigation were terminated before the end of the irrigation season, and irrigators, who were relying in part on diversions from the Portneuf River, had to rely solely on ground water as an alternate supply. Smaller volumes of water in the Chesterfield Reservoir since the 1990s indicate a growing demand for ground-water supplies.