Processes that structure subarctic marine communities, particularly in glaciated regions, are not well understood. This understanding is needed as a baseline and to manage these communities in the face of future climate-driven changes. This study investigates two coastal regions of Southeast Alaska with the goals to (a) identify and compare patterns of subtidal community structure for macroalgal, fish, macroinvertebrate (>5 cm), and small epibenthic invertebrate (<5 cm) communities between inner coast and outer coast sites and (b) link patterns of community structure to habitat and environmental parameters. Species assemblage and benthic habitat data were used to compare species diversity and community composition at 6 m and 12 m depths at nine inner coast and nine outer coast sites. Multivariate analysis was applied to reduce environmental variables to major gradients, to resolve community structure, and to relate community structure to habitat and environmental variables. Increased salinity and decreased temperature at outer coast sites compared with inner coast sites were associated with community structure, with greater species diversity at outer coast sites at 6 m depth. Invertebrate community composition was associated with benthic habitat, including crust and coralline algae for macroinvertebrates, and algal cover and substrate for small epibenthic invertebrates. This research suggests that marine communities in glaciated regions are strongly influenced by freshwater input and that future climate-driven changes in freshwater input will likely result in marine community composition changes.