Pacific salmon influence stream ecosystems during their annual spawning runs by providing streams with marine-derived nutrients and by disturbing biota during upstream migration and the construction of spawning nests.  Watershed alteration, such as timber harvest, may modify the balance between nutrient enrichment and physical disturbance by changing the physical stream environment.  We assessed the interaction between salmon and the physical stream environment using a hierarchical design that encompassed the scales of riffle, reach, and stream in four watersheds on Prince of Wales Island, Alaska, subjected to different levels of timber harvest.  Before the salmon run, algal abundance (chlorophyll a) was low and similar across all spatial scales.  The arrival of salmon introduced a high degree of chla variability among riffles (range, 43.4mg/m²) and reaches (range, 28.8mg/m²) within pristine streams (range, 18.8 mg/m²).  In contrast, salmon had a less pronounced effect on riffles (range, 23.5mg/m²) and reaches (range, 8.8mg/m²) in harvest-impacted streams (range, 2.1 mg/m²).  Streams in harvested watersheds lacked the spatially complex physical environments typical of pristine streams.  Collectively these results suggest that salmon create a patchy distribution of algal abundance across multiple spatial scales; this variability closely mirrored the heterogeneity of the physical stream environment.