Timber harvest modifies the physical stream environment in ways that could alter ecological responses of streams to salmon runs. We examined this possibility in seven Southeast Alaska streams, the watersheds of which have been harvested of their timber to varying degrees (6%-85% of the watershed area harvested). We measured physical attributes of the stream channel, salmon inputs, and periphyton response to the presence of salmon. Prior to salmon migration we observed a positive relationship between chlorophyll a and the percentage of the watershed harvested of its timber (r²=0.69, p=0.02). During the salmon run, however, this relationship became negative (r²=0.63, p=0.03), but did not persist after the salmon run (r²=0.01, p=0.82). These patterns reflect a reduction in sediment size along the timber harvest gradient, and a strong positive relationship between sediment size and chlorophyll during the salmon run (r²=0.95, p=0.005). Our results illustrate how timber harvest alters the physical stream environment and can transform the dominant role of salmon from one of nutrient enrichment to one of physical disturbance, as mediated by changes in sediment size. By dampening the positive effect of salmon spawners on primary producers, timber harvest can impact an important resource linkage between marine and stream ecosystems.