Glaciers have pronounced long- and short-term effects on nearshore marine ecosystems. Concerns exist about possible changes that may occur to nearshore habitats with the pronounced climatic alterations in subarctic and high-latitude environments. The present research studied the effects of glacial discharge on kelp bed community structure by comparing environmental conditions on one more exposed and one less exposed shore in a subarctic Alaskan estuary. Inorganic sedimentation, abrasion, and percent sand/silt substrate were significantly higher on the more exposed shore than the less exposed shore. Light intensity, salinity, nitrate concentrations, and hard substrate cover were significantly lower on the more exposed shore. Kelp bed communities on the more exposed shore contained only one kelp species, Saccharina latissima, versus five kelp species on the less exposed shore. Taxonomic richness and overall organism abundance were significantly lower on the more exposed shore. Salinity, nitrate, inorganic sedimentation, and abrasion were identified as important drivers of kelp communities that are dynamically influenced by glacial discharge. In contrast, other drivers, such as hard substrate and rugosity, reflect existing differences between the two shore environments that are not influenced on short timescales by glacial discharge. While it is currently difficult to separate the relative roles of these two types of drivers on kelp bed communities, increased rates of glacial discharge due to climate change may exacerbate specifically the effects of the dynamic drivers and further decrease species richness in kelp bed communities in high-latitude estuaries.