A prioritization strategy involving evaluation of information needs, expert input, and landscape features was used to direct aquatic habitat surveys and fish distribution mapping efforts in 12 high priority watersheds in Southeast Alaska. During 2001–2003 over 3,600 GPS waypoints were captured while mapping 171.5 km of stream, river, side channel, and lake or pond habitat. Habitats were classified into distinct reaches according to fluvial process group and channel type. The average gradient, total length, and density of large woody debris and macro pools were calculated for prioritized waters within watersheds. Mapping of salmonid distribution patterns often occurred concurrently with surveys to map and classify stream networks, depending on individual watershed information needs. A total of 385 GPS waypoints allowed mapping of over 450 instances of fish capture or effort. Nearly 1,800 anadromous and resident salmonids were captured or observed during these efforts. The collection of spatially specific fish and fish habitat data would provide updated information helpful in addressing a variety of salmon and salmon habitat issues.