Diatom colonies were established on glass slides in Rouge River and Wilmot Creek before application of the lamprecide 3-trifluoromethyl-4-nitrophenol and their abundance was monitored for 21 and 55 d, respectively, after treatment. A total of 105 species of diatoms were identified from the Rouge River; of these, 23 were particularly abundant. Samples from Wilmot Creek yielded 80 species, of which 21 were dominant. Growth of the diatom community at the treated sites of Rouge River declined following chemical treatment, 8.7 mg 3-trifluoromethyl-4-nitrophenol per litre, but recovered within 21 d. Community structure and abundance in Wilmot Creek were not significantly altered by the addition of 5.3–6.7 mg 3-trifluoromethyl-4-nitrophenol per litre. No species identified from either stream exhibited particular sensitivity to the concentrations of 3-trifluoromethyl-4-nitrophenol applied. Temporal and spatial patterns of change are discussed.