Benthic diatom assemblages from 179 streams and 98 lakes in Sweden were compared to identify differences in taxonomic composition, growth form, cell size, diversity and richness, and ultimately, to assess the effects of differences between streams and lakes on assessments. Streams and lakes with similar environmental background variables were chosen to avoid an overriding effect of factors, such as nutrients and pH, on taxonomic composition. Generic and species composition differed significantly between streams and lakes. Richness was significantly higher in lakes than in streams, and the average diatom cell was significantly longer in streams than in lakes. No other measures analyzed differed significantly. Diatom assemblages in both habitats were related to pH and nutrients, and the diatom indices studied responded similarly to the main environmental gradients in both habitats. Thus, despite differences in taxonomic composition between streams and lakes, the resulting diatom assemblages are similar, enabling use of the same diatom indices in both habitats.