The heterogeneous nature and widespread anthropogenic impacts to wetlands in the Willamette Valley, Oregon, pose challenges to bioassessment of these systems. The purpose of this study was to examine diatom species patterns in relation to environmental variables in wetlands, and to compare a diatom-based wetland classification to a hydrogeomorphic (HGM) wetland classification. Surface sediment diatoms, water quality, physical habitat, and surrounding land use characteristics were assessed for 92 wetlands. A total of 419 taxa were identified. Taxa richness was high (mean = 54, range 15–94) and dominance by a single taxon at a site was low (mean = 27%, range 7%–78%). Assemblages were dominated by tychoplanktonic taxa (e.g., Staurosira construens) and periphytic taxa (e.g., Fragilaria capucina and Achnanthidium minutissimum). Non-metric multidimensional scaling and correlational analysis showed that diatom assemblages were correlated with water depth, summer and winter total phosphorus, soluble reactive phosphorus, and turbidity. Diatom-based classification of wetlands produced four statistically significant groups that corresponded to within-wetland water depth, nutrient levels, and turbidity. Diatom-based wetlands classification did not agree with a priori HGM classification. Diatom assemblages and common species were similar between depressional and riverine-impounded wetlands. Our results suggest that, despite regional heterogeneity in both diatom assemblages and environmental conditions, diatoms can be useful indicators of water quality and habitat conditions in riverine and depressional wetlands. HGM classification may be too coarse to elucidate patterns of diatom community structure and conditions of the habitat in these anthropogenically-impacted wetlands.