In streams, reach-scale physical habitat (i.e., pool, run, riffle, cascade; hereafter mesohabitat) is viewed as an important control on the distribution of organisms. However, there is limited understanding of stage-specific mesohabitat associations in species with complex life histories and of associated causes and population-level implications of these distribution patterns. In intensive field surveys, I found that larvae and adults of the stream salamander Gyrinophilus porphyriticus (Plethodontidae) displayed similar associations with pools and riffles. However, larvae were negatively associated with cascades and adults were negatively associated with runs. Adults had no effect on the survival, growth, or activity of larvae in a controlled experiment, suggesting that stage-specific negative associations were not a function of intraspecific interactions. These negative mesohabitat associations may be related to the size-distribution of interstitial spaces in cascades and runs, which were biased against larval and adult body sizes, respectively. My results indicate that incorporating reach-scale habitat structure in sampling programs is critical for accurate assessments of stream amphibian populations, and that perturbations altering reach-scale habitat structure may differentially affect life history stages of G. porphyriticus.