Successful reintroductions of endangered species rely on comprehensive knowledge of habitat requirements across spatial and temporal scales. To inform designs of reintroduction programs, we studied habitat selection of the federally endangered Sierra Nevada yellow‐legged frog (Rana sierrae) in streams in its northern range. We quantified multi‐scale habitat use across diverse streams, habitat types within streams, and seasonal flows. In one intermittent stream, we compared habitat selection between wild and captive‐reared frogs that were released as a population augmentation. We analyzed habitat selection of seasonal habitat unit types (e.g., pool, riffle, cascades) and dimensions, and microhabitat hydrology and cover. R. sierrae appeared able to meet its ecological requirements in a variety of habitats. Study streams ranged from third‐order perennial streams to first‐order intermittent headwater creeks. Perennial streams retained a variety of habitats across flows whereas intermittent streams dried to just a few pools. Frogs used all seasonal habitat types but selected deeper pools most often relative to available habitats in intermittent streams and selected riffles or showed no preference in perennial streams. Frogs avoided fast deep‐water microhabitats, but, otherwise, preferred flowing water or deeper water without flow. Our results suggest that diverse streams can be considered candidates for reintroductions. Within intermittent streams, deeper perennial pools may provide more stable release sites, whereas non‐pool habitats may be safer in perennial streams with fish. Importantly, captive‐reared frogs selected similar habitats as wild frogs, suggesting that captivity does not alter habitat selection behaviors post‐release and that reintroduction designs for this species can be based on wild frog preferences. By improving our understanding of how habitat use varies among different types of streams and differs seasonally in response to changing habitat conditions, our results inform the design of effective reintroduction programs for frogs in streams.