Seventy-eight taxa of diatoms were identified from thc epiphytic community of Cladophora glomerata in the Colorado River through Glen and Grand Canyons. Achnanthes affinis, Cocconeis pediculus, Diatoma vulgare, and Rhoicosphenia curvata made up 80% of the diatom epiphyton community within 15 km of Glen Canyon Dam, Arizona. However, these taxa made up only 33% of the periphyton community 354 km downstream. Mean total diatom density associated with Cladophora glomerata was significantly reduced at each sequential station downstream. Diatom density decreased and community composition of diatoms changed with increasing water depth in the river channel. Cell densities of D. vulgare, C. pediculus, and R. curvata decreased markedly at Lees Ferry following a 3-month period of fluctuating flow during October through December 1985.