Conservation and management of headwater streams amid rapid global change require an understanding of the spatial and environmental factors that drive species distributions and associated ecosystem processes. We used a hierarchical analytical framework to model effects of catchment-scale topography and wetland geomorphic classes on stream physical habitat, chemistry, and macroinvertebrate and fish communities in 30 headwater streams across the Kenai Lowlands, southcentral Alaska, USA. We identified 135 macroinvertebrate taxa, 122 of which were aquatic insects, of which 79 were dipterans. We collected only 6 species of fish, but juvenile coho salmon and Dolly Varden were collected in 17 and 25 of the 30 streams and reached densities >500 and 1300/km, respectively. Flow-weighted slope, an indicator of water residence time and gradient, was the best catchment-scale correlate of macroinvertebrate and fish community structure, and its effect was mediated by wetland geomorphic classes and numerous water chemistry, substrate composition, and channel geomorphology variables measured at the reach scale. Many macroinvertebrate taxa showed high fidelity to different levels of the topographic gradient, resulting in high β diversity but relatively similar levels of α diversity across the gradient. Juvenile salmonids were segregated among streams by both species and age classes. Coho salmon fry and parr (<10 cm total length [TL]) had significant unimodal distributions that peaked in streams with intermediate slopes and gravel substrate, whereas presmolts (≥10 cm) were found only in lowest-sloping streams with mostly peat substrate and deep, slow channels. Large Dolly Varden (≥8 cm) were found across the entire gradient but were most abundant in high-sloping catchments, whereas small Dolly Varden (<8 cm) followed a similar distribution but were absent from the lowest-gradient sites with low flow velocity, dissolved O₂, and gravel substrate. Predictive modeling indicated that all of the 547 km of headwater streams in the study area might serve as potential habitat for ≥1 species and age class of salmonids. Our study should assist in development of catchment management tools for identifying and prioritizing conservation efforts in the region and may serve as a framework for other studies concerning biodiversity and focal species conservation in headwater streams.