Scientific Investigations Report 2006–5230
U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2006–5230
A list of priority streams based on input from the Interagency Technical Workgroup was provided by the Bureau of Reclamation. USGS conducted a reconnaissance on each stream to locate diversions and select potential study sites. The Bureau of Reclamation and USFS assisted in identifying private landowners and obtaining permission to access their land. PHABSIM study sites in the upper Salmon River Basin were selected following guidelines described by Bovee (1997). According to these guidelines, a geographic hierarchy is used to represent a study area in PHABSIM. The first-order subdivision of the study area is the stream segment. Stream segments typically are long sections of stream with a uniform flow regime and consistent geomorphology. Each stream segment, can have several habitat-related subdivisions, including representative reaches, mesohabitats, and microhabitats.
Representative reaches and mesohabitat types describe the stream segment and make up the second-order division of the study area. A representative reach is about 10 to 15 channel widths in length and typically contains many or all of the mesohabitat types present in the entire segment. Proportions of the mesohabitat types in the reach also are assumed to be the same as their proportions in the segment. Mesohabitats are short sections of stream, usually with a length about the same magnitude as the width, and have unique characteristics that distinguish them from other mesohabitat types. Mesohabitat types are identified through a process known as mesohabitat typing, which is an inventory of each mesohabitat proportion in a segment. Mesohabitat types commonly are delineated by localized slope, channel shape, and structure and generally are described as runs, riffles, or pools. Collectively, all the mesohabitat types represent the stream segment.
Either the representative reach or mesohabitat typing typically is used to describe the stream segment. In 2005, due to difficulty gaining access to private lands to walk streams for measuring mesohabitats, representative reaches were selected based on field reconnaissance from nearby public access areas and the use of topographical maps. When possible, a stream length exceeding 40 times the wetted channel width was walked to select a representative reach to assess. The various mesohabitats were measured in each reach and transects were weighted in the PHABSIM model according to their relative lengths in the reach.
Although a mesohabitat type often is described simply as a run, riffle, or pool, it can be stratified into finer subdivisions to describe the stream segment more accurately. Often, these finer subdivisions take into account varying degrees of slope, width, velocity, and depth. Eight mesohabitat categories were used in this study and represent backwater (pools) and varying degrees of slopes (riffles and runs) in both narrow and wide channels (fig. 2). Specifically, these mesohabitats included shallow and deep pools representing backwater with a hydraulic control. Slopes, designated as low, moderate, or high were measured qualitatively based on professional judgment and are not transferable between streams (for example, high slopes on one stream may or may not compare to high slopes on another). Because of the large variation in stream types, mesohabitat typing was based on relative changes in each stream. The overall goal of this approach was to categorize major habitat types present in each segment and represent them in the PHABSIM modeling by weighting their relative importance.
PHABSIM study sites, the third-order division of a study area, describe either the representative reaches or the mesohabitat types. The study sites are divided longitudinally by stream cells and transects. Transects typically represent the most common habitats and hydraulic controls in each reach. Generally, one to two transects were selected to represent each major mesohabitat in each reach. Cell boundaries are defined by transects and verticals perpendicular to streamflow. When mesohabitat types are used to describe the stream segment, transects are established at the study site to represent the mesohabitat type and are weighted according to the proportion of the mesohabitat type in the representative reach. Mesohabitats making up less than 10 percent of the representative reach generally were not included in the assessment.
Transects, the fourth-order division of a study area, are subdivided by lateral stream cells with longitudinal boundaries and verticals along which measures of microhabitat are made. Microhabitats usually are shorter than one channel width and represent a relatively homogeneous area used by an individual fish (Bovee, 1997). Examples of microhabitat include undercut banks, velocity shelters behind boulders, and woody debris.
Stream sites were established downstream of all diversions on each stream to evaluate the cumulative effect of multiple diversions. Additional study sites on the same stream were selected downstream of other upstream diversions if significant amounts of water (>10 percent of streamflow) were being diverted.
Shallow riffle habitats that potentially could create a bottleneck to passage were evaluated at each study site. One or more transects were placed across these areas at each study site to evaluate discharge relations and stream depth across the entire stream width.
Data were collected at verticals along transects to represent hydraulic and geomorphologic conditions in each cell in a mesohabitat type. Water-surface elevations were determined at each transect for at least two measured discharges. One additional stage-discharge pair was collected at some transects when cross-sectional data were collected at verticals in the transect.
Data were collected at about 30 to 40 verticals to define the habitat features of each transect. At each vertical in a transect, depth and mean velocity were measured, and cover and substrate types were determined. Velocity calibration sets were collected during two periods to represent a range of summer streamflows. Cell width was determined from the spacing of the verticals. Channel structure and hydraulic variables were collected using standard USGS procedures described by Benson and Dalrymple (1967) and Rantz (1982).
Hydrologic information for each study site was expressed using the estimated monthly 80-, 50-, and 20-percent exceedance discharge statistics. These statistics were estimated for each site using regional regression equations from Hortness and Berenbrock (2001). The regional regression equations use basin characteristics such as drainage area, precipitation, and basin slope to estimate streamflow statistics at ungaged sites. Exceedance discharges indicate the discharge that is expected to be equaled or exceeded a specific percentage of the time for a specific month or other time period. Estimates generated by these regional regression equations represent natural or unregulated streamflows.
Substrate and cover were also recorded. Substrate types were identified by visual observation and were classified as organic detritus, silt, sand, small gravel, coarse gravel, cobble, boulder, bedrock, and aquatic vegetation. When more than one substrate type was observed at the vertical, such as gravel and cobble, the dominant substrate was determined. Instream cover that provided velocity shelter and (or) protection from predators for fish was determined across each transect. Types of cover included woody debris, undercut banks, large substrate (for example large gravel, boulder, or large cobble), aquatic vegetation, and overhanging vegetation (Raleigh and others, 1986). To characterize stream shading, percentage of canopy opening was estimated at each transect with a clinometer following procedures described by Fitzpatrick and others (1998).
Onset TidbiT™ data loggers were used to record stream temperature at several locations throughout the study area. Data logger deployment and data collection followed procedures outlined by Stevens and others (1975) and Zaroban (2000).
To capture the natural thermal regime and to assess the effects of diversions on stream temperature, data loggers were deployed spatially throughout a stream. Where permission to access private land was granted, a data logger was placed far enough upstream of all diversions to avoid possible effects of diversions. Data loggers also were deployed at study site locations and near the stream’s mouth. Deployment consisted of selecting a well-mixed location in the stream, usually in the thalweg below a riffle, and attaching the data logger to a steel rod that was driven into the streambed. Data loggers were placed at mid-depth out of direct sunlight when possible and were programmed to record stream temperature hourly.
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