|Periphyton assemblages on the Stony River, a high-gradient stream in the Potomac drainage of Grant County, WV, were assessed. Periphyton samples were collected from nine sites along the mainstem and in two tributaries. Chlorophyll-a, dry weight, taxonomic identifications, and bioaccumulated metals concentrations data were compiled. These data were related to water quality parameters measured at each site during the study. Fuzzy C-means and k-nearest neighbor clustering on the combined, normalized dataset produced similar results. Clustering separated species occurring in each tributary from each other and those dominating the mainstem. Nearly every bioaccumulated metal was associated with one of these tributary clusters; phosphorus and silicon were exceptions with silicon being associated with diatoms. The remaining clusters formed a continuum of community composition along the mainstem different from the spatial arrangement of sites. Additionally, taxa occurring in small quantity force clusters to form near the center of the data-space, confounding results.