We evaluated the species distribution, abundance, and habitat relationships of salmonids in small first‐ to second‐order headwater streams in southeast Alaska. Streams were separated into three zones based on gradient and sampled during the spring, summer, and fall. Dolly Varden Salvelinus malma were found in all streams where fish were present. They were the dominant species in moderate‐ (mean gradient = 5.5%) and high‐gradient (mean gradient = 12.9%) zones. Coho salmon Oncorhynchus kisutch fry and parr were the dominant species in the low‐gradient zone (mean gradient = 3.1%) but were present in higher‐gradient zones. Small numbers of steelhead O. mykiss parr were present in all three zones in the spring and fall. Few were captured during the summer. Coastal cutthroat trout O. clarkii were found primarily in one stream and in all three zones. The density of all species decreased as gradient increased. Anadromous Dolly Varden in spawning condition were observed in the fall up to the highest accessible locations in four streams. Salmonids use high‐gradient reaches when pools are present and accessible. Headwater tributaries comprise a large proportion of most southeast Alaska watersheds, and the combined contribution from all of these tributaries to the fish community may be large. The results from this study underscore the importance of maintaining access for fish throughout watersheds and into small high‐gradient streams.