River ecosystems in the arctic are expected to undergo significant change during this century, with temperatures increasing at twice the global average and substantial shifts in discharge and nutrient supply predicted. To provide insight into the potential consequences of these changes to aquatic ecosystems, we assessed temporal patterns of nutrient availability, epilithic biofilms and invertebrate abundance and production in the Kuparuk River in arctic Alaska (Arc-LTER). Epilithic chlorophyll over a 31-year period was shown to be controlled, in part, by the discharge regime of previous year, i.e. a ‘legacy effect’, but was not related to the significant declines in total dissolved phosphorus documented over the 19-year available record. Additive mixed-model analyses revealed non-linear and species-specific responses of invertebrate population abundances to temperature and discharge over the 31-year record. A 12-year record (2001-2012) shows epilithic chlorophyll, but not temperature, is a significant and positive predictor of invertebrate secondary production (R2 = 0.58). These data suggest that within the study period, discharge and its effects on basal resources are the major determinants of arctic river structure and function.