We sampled the larvae of a rare streamside salamander, Eurycea junaluska, across a range of stream sizes to determine habitat use patterns at both reach (75-m length of stream) and watershed scales (i.e., the network of streams draining fourth-order watersheds and their relationship to the larger river channels). An information-theoretic approach to logistic regression indicated an association between larval E. junaluska occurrence and lower gradient (<2%) reaches with a relatively high amount of silt substrata. At the watershed scale, these types of reaches were associated with moderate-sized streams and smaller low gradient streams crossing the floodplain of larger rivers. Our results suggest that E. junaluska prefers larger stream and river channels and that past channel impoundment and modification has resulted in fragmentation of remaining populations.