# River-Wide Habitat Availability for Fish Habitat Guilds: Implications for In-Stream Flow Protection
## 2 Materials and Methods  
### Niobrara River  
The Niobrara River basin covers approximately 32,600 km\({}^{2}\) with a large portion (90%) of the Niobrara River traversing through northern Nebraska, USA (Figure 1). The Niobrara River is an alluvial river with distinct hydrogeomorphic characteristics--alternating wide and narrow stream valleys (i.e., <300 m to >900 m) and channel widths (i.e., <10 m to >300 m)--along the longitudinal gradient of the river [17]. The Niobrara River is a groundwater dominated system receiving inflow from the Ogallala and High Plains aquifers (17; 18). Additionally, seasonal precipitation patterns induce variation in river discharge. Mean monthly discharges--based on mean monthly discharge data from 1938 to 2016--range from 34 m\({}^{3}\) s\({}^{-1}\) (SE = 1.27; August) to 72 m\({}^{3}\) s\({}^{-1}\) (SE = 2.35; March) in the eastern portion of the basin near the confluence with the Missouri River (Figure 2; USGS Gauge 06465500). Water development within the basin (e.g., diversions and impoundments) has caused reductions in discharge and channel constraining (17). However, the contribution of groundwater and seasonal precipitation patterns maintain base discharges and seasonal variability within the Niobrara River (17; 19) unlike many other Great Plains systems.  
We chose one study site within each of sixteen river sections (i.e., total of 16 sites) following recommendations from previously quantified habitat breaks (17) as well as foot and aerial reconnaissance surveys along the length of the Niobrara River. We selected each study site using previously collected cross-sectional measurements from (17). The proportion of HMUs at each site was similar to the larger-scale section based on a cross-section analysis of each of the 16 sections. To evaluate the section representativeness of each study site, we used boxplots of the associated morphometric data. Morphometric data included channel slope, sinuosity, width, ratio of channel wetted width to total channel width, coefficient of variation of channel width, ratio of channel width to valley width, the number of channels, mean stream power, and the 90 th percentile stream power (17). We compared box plots of the section and site to ensure that the median, lower quartile, and upper quartile were similar. If not similar, the study site was expanded until section and site boxplots were similar. If a study site expanded beyond 6 river kilometers (rkm), a new site was selected and the process of measuring site representativeness was repeated. The sixteen sections (Figure 1) lie within three river segments that differ by fish community diversity as well as channel morphology, channel width, and valley width (17). Segment 1 (sections 1-3; 193 rkm, mean channel width = 313 m, mean valley width = 939 m) includes the lower Niobrara River and delta region upstream to Spencer Dam. Segment 2 (Sections 4 and 5; 309 rkm, mean channel width = 37 m, mean valley width = 277 m) includes the braided sites between Spencer Dam and Norden Chute. Segment 3 (sections 6-16; 230 rkm, mean channel width = 6 m, mean valley width = 991 m) includes the remainder of the Niobrara River west of Norden Chute to Box Butte Reservoir dam.  
Figure 1: Fish sample sites (filled circles) and locations of river sections (alternating blue and white areas along river) representing unique hydrogeomorphic conditions and gauging stations (filled triangles) in the Niobrara River located in Nebraska, USA. Inset shows the Niobrara River basin outlined in gray. River discharge is from west to east.