Forest management operations greatly influence stream habitats. Canopy clearing and subsequent canopy development during succession, site preparation, and ditching alter the light environment, and increase sediment inputs and nutrient exports from upland and riparian soils to streams. These physicochemical changes affect aquatic biofilms and metabolic rates, and in this study, we tested their individual and combined effects. We used 12 artificial streamside channels, together with a field survey of nine streams in and around clear-cuts, to assess the effects of shading, substrate composition, and nutrient addition on biofilm biomass and composition, as well as metabolic rates. We found that biofilm biomass and gross primary production (GPP) were light limited in channels under 70% canopy shading. Nitrate additions at this shading level only marginally increased autotrophic biomass, while the rates of respiration increased 10-fold when carbon was added. Open (unshaded) channels had three times higher rates of GPP compared with channels with 70% shading, and autotrophic biomass was twice as high, largely caused by the colonization of filamentous green algae. These changes to biofilm biomass, composition, and GPP were caused by differences in light alone, as temperature was not affected by the shading treatment. Notably, higher rates of GPP led to no positive effect on net ecosystem production. Further, fine-grained substrates negatively affected GPP as compared with stone substrates in the experimental channels. In the surveyed streams, the negative effects of fine-grained substrates exceeded the positive influence of light on biofilm biomass. Altogether, our results highlight the need for riparian management that protects headwaters from unwanted stressors by focusing on preventing sediment erosion and carbon transport in clear-cuts, while providing variable shade conditions in second-growth forests.