Diatoms were collected at 165 stream, river, wall seep, and pond/lake sites in 9 counties in northwest and north central Washington, including the Olympic Pennsisula, over a 5-year period. Four hundred and fifteen species in 77 genera were identified. Species assemblages were compared to altitude, physicochemical factors, aquatic habitats, and land use on west and east sides of the North Cascade Range. Species richness averaged 30.5 per site on the west side and 43 on the east side. Diatom species richness showed significant positive correlations to total nitrogen, total phosphorus, pH, specific conductance, channel embeddedness, and water temperature, and a significant negative correlation to percent canopy cover. A multilevel hierarchical clustering model separated streams, rivers, wall seeps, and ponds/lakes into geographic and land-use regions based on diatom assemblages. A multimetric index (diatom tolerance index [DTI]) was developed to determine environmental tolerance levels for diatom species over a large number and variety of sites. The index performed well in distinguishing between the role of embeddedness, total nitrogen, total phosphorus, and specific conductance on the distribution of diatom species and showed close agreement between land use and diatom distribution. These DTI values provide baseline information for monitoring changes in ecosystem health in drainages throughout Washington landscapes. Didymosphenia geminata occurred in 46% of the streams and rivers sampled and ranged from <1% to 27% in relative abundance, but it was not collected in ponds/lakes or wall seeps. Didymosphenia geminata density showed a significant positive correlation to suspended sediment and significant negative correlations to altitude and total nitrogen. This invasive alga attained a higher average relative abundance in rivers compared to streams and occurred in 28% of the sites examined west of the Cascade Range compared to 63% of the sites east of the Cascades.