The taxonomy, community structure, microcommunity structure and standing crop of benthic diatom communities were investigated at a site representative of the upper Laurentian Great Lakes. Spatial and temporal variations on natural substrates were examined at a single site to provide basic information on these poorly studied communities. The flora was studied by employing light microscopy, permanently mounted voucher specimens and a file containing photomicrographs of the specimens. The flora exposed by this study contained 425 taxa representing 40 genera. Sixty-four of these are previously undescribed, 41 are new Great Lakes records and 27 of these are new North American records. Most of the taxa are indifferent to alkalibiontic and many are boreal and alpine in distribution. Information-theory diversity generally increased from the surface to 20 m and decreased slightly at 31 m. During summer, diversity remained low to 20 m, reflecting the intrusion of the mid-depth diatom assemblage to thermocline depth. Cluster analysis of samples demonstrated that distinct mid-depth and deep-water diatom associations existed throughout the year, and several shallow-water associations existed during spring, sumner and fall. Cluster analysis of taxa showed that unique groups were present in the shallow, mid-depth and deep sample clusters. The groups of highly correlated species were generally associated with distinct substrate types, with the mid-depth cluster on sand and the deep cluster on sand covered by floc. All natural substrates examined with scanning electron microscopy, except the red alga Bangia atropurpurea, supported extensive growth of diatoms, other algae and bacteria. Unique epipsammic, epilithic and epiphytic associations have been described. Seasonal peaks of extracted chlorophyll a occurred at 5 m in winter and spring, 20 m in summer, and 10 m in fall.