Migrations by spawning Pacific salmon (Oncorhynchus spp.) deliver a major ecosystem resource subsidy of marine nutrients to nutrient-poor streams of southeastern Alaska. I examined the effects of these salmon-derived nutrients (SDN) on surface water chemistry and epilithon biomass and metabolism in streams and estuaries in southeastern Alaska. With addition of salmon material (either from salmon runs or artificial salmon products), fluxes of streamwater ammonium (NH4+-N) and soluble reactive phosphorous (SRP) increased significantly in streams and estuaries, whereas nitrate and dissolved organic carbon did not. Increases in NH4+-N and SRP were significantly larger in estuaries than in streams, suggesting that SDN were being exported from freshwater reaches to estuaries. Responses in epilithon biomass and productivity in streams and estuaries to addition of salmon material varied widely across systems. Complex interactions among environmental and biological characteristics, such as irradiance, ambient nutrients, hydrology, and salmon spawner disturbance, likely regulate epilithon growth in these systems.