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Climate change is expected to alter disturbance regimes and biogeochemical cycles that underlie the structure and function of ecosystems worldwide. In the Arctic, rapid warming is already affecting these processes via changes in precipitation and thawing permafrost. We assessed how anticipated changes in disturbance regimes and nutrient availability may affect an arctic river ecosystem (Kuparuk River, Alaska) by analyzing temporal patterns of biofilm chlorophyll mass and macroinvertebrate community structure and productivity. Our study incorporated an upstream reach (sampled 2001–2012) and a downstream reach (sampled 2011–2012) to which phosphorus (P) was added to simulate increases in nutrient supply that are anticipated as permafrost thaws. Greater hydrologic disturbance during the open‐water season correlated with reduced algal biomass and invertebrate secondary production (range ∼ 2–7 g DM m⁻²yr⁻¹) in the following spring and summer. Bed disturbing flows also altered macroinvertebrate community structure with distinct “high‐flow” and “base‐flow” assemblages documented. Recovery time was shorter for chlorophyll mass and macroinvertebrate production (∼ 1 yr) than community structure (∼ 3 yr). Experimental P‐addition increased algal biomass and invertebrate production, but also resulted in a third macroinvertebrate assemblage dominated by mobile grazers rather than filter‐feeders. Our results suggest that a decrease in the return interval for bed disturbing floods to < 4 yr will result in persistent changes in macroinvertebrate community structure and fundamental alterations to the food web. These results also demonstrate how arctic river communities may be affected by increases in the magnitude and variability of river discharge and nutrient supplies that are anticipated as the climate warms.