Aquatic algal communities are sensitive to environmental stresses and are used as indicators of water quality. Diatoms were collected from three streams that drain the Great Marsh at Indiana Dunes National Lakeshore. Diatom communities, water chemistry, and land use were measured at each site to test the hypothesis that differences in land use indirectly affect diatom communities, through changes in water quality. Relationships among these variables were examined by correlation, cluster, and detrended correspondence analysis. Several water chemistry variables were correlated to several land-use categories. Diatom species diversity was most variable in disturbed areas with poorer water quality and was correlated with land use and total alkalinity, total hardness, and specific conductance. Sites within each stream were grouped in terms of their diatom assemblage by both cluster and detrended correspondence analysis with but two exceptions in Dunes Creek. Diatom communities in the three streams responded to land use through its effects on water quality. The results of this study demonstrate the use of diatom assemblages as indicators of water quality, which can be linked to land use in a watershed.