Management of freshwater aquatic ecosystems requires an understanding of interactions among biotic and abiotic components on the landscape. Quantitative information on individual habitat metrics and the cumulative habitat associated with freshwaters allows comparisons across spatial and temporal scales. The stream habitat survey methods described in this manual will assist in the collection of spatially-explicit data associated with meaningful biological and hydrological attributes that are common in Southeast Alaska. The reach-based protocol outlined in this manual provides a means for documenting existing channel and riparian conditions at the individual reach scale, juxtaposed with fish species and life stage distribution across the watershed being surveyed. Providing a spatial context to all physical and biological data components will enhance the ability of managers to conduct more meaningful landscape-level resource assessments, as well as their ability to quantitatively track and manage change over time.