Ecology of the Sierra Nevada Yellow-Legged Frog (Rana sierrae) is well understood in high elevation lakes, but data on habitat preferences in stream-dwelling populations are lacking. We sought to expand understanding of stream habitat use by R. sierrae by investigating habitat suitability at the microhabitat and reach scales. We collected habitat availability and use data during 2016–2017 at five stream sites representative of geomorphic diversity in the northern Sierra Nevada mountains of California. At each frog use and availability location, we collected data on geomorphic unit type (e.g., riffles, pools), water depth, water velocity, substrate (e.g., gravel, cobble), and percent cover, including herbaceous, canopy, and total cover. Bootstrapped logistic regression models for all study sites combined indicated water depth and velocity were the strongest predictors of post-metamorphic (adult and subadult) use by R. sierrae, while substrate and total cover provided moderate improvement in microhabitat use predictions. Specifically, adults had the highest probability of use in microhabitats with <0.3 m depth and <0.1 m s^–1 velocity. For tadpoles, we found velocity was the strongest microhabitat predictor for all study sites combined, with the highest probability of use in habitats with <0.01 m s^–1. Site-level models highlighted the relative importance of non-hydraulic habitat variables, such as cover, when suitable depth and velocity conditions occurred. At the reach scale, we found hydraulic conditions varied widely in geomorphic units over time, but suitable microhabitat conditions emerged in differing geomorphic units as flows changed over the season. These data indicate that R. sierrae, like other ranid species, may be limited by hydraulically suitable habitat availability, but habitat preferences can be met in a variety of stream reaches when variations in flow conditions over time and space are considered.