Spatially patchy and temporally varied cycles of timber harvest across a landscape may have subtle effects on stream conditions that are difficult, but important, to assess. The objective of our study was to examine the relationship between benthic diatom composition and timber harvest in coastal Oregon watersheds. Physical habitat conditions, water chemistry, and periphyton composition were characterized for 46 sites from 2 subbasins with different timber harvest intensities (0.3 km²/y vs 3 km²/y, between 1972–1998). Landscape variables including geology, vegetative cover types, and harvest intensity, were quantified for the watershed upstream of each sample point. Nonmetric Multidimensional Scaling analysis of periphyton composition showed that the 1^st axis was primarily driven by Achnanthidium minutissimum (r = −0.91) whereas the 2^nd axis was driven by Nitzschia inconspicua (r = 0.77). The 1^st axis was positively correlated with % of upstream area harvested between 1972 and 1998 (r = 0.54) and water-quality variables such as total P (TP) (e.g., r_TP = 0.74). A subset comparison (n = 12) between harvested (30% harvested 1972–1998, n = 6) and unharvested (0% harvested 1972–1998, n = 6) watersheds with similar geology (>80% basalts), broadleaf vegetative cover (8–35% broadleaf), and other reach-scale characteristics revealed higher total N, TP, turbidity, and conductivity in the harvested than the unharvested watersheds (p < 0.05). Shannon diversity and species richness also were higher in the harvested group (p < 0.05). Our data suggest that diatom assemblages may be useful in assessing the long-term impact of timber harvest within coastal Oregon watersheds.