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This study sought to understand the performance of arctic treatment systems and the impact of wastewater effluent on benthic invertebrate communities in arctic receiving water habitats. Effluent quality and benthic impacts were monitored in the receiving water of five communities across Nunavut that differed in the type and level of treatment achieved by wastewater infrastructure, the volume of effluent and receiving water mixing environment. We detected minimal impacts to benthic communities (<225 m linear distance from the effluent source) in four out of the five communities (Grise Fiord, Kugaaruk, Pond Inlet, and Pangnirtung), where the population was <2000 people. In these small communities impacts were characterized by increases or decreases in species richness, diversity, evenness, and density, and some differences in benthic species composition. This was in contrast to benthic sediments in Iqaluit (population 6699), which were devoid of benthic fauna up to 580 m from the effluent source in response to sediment anoxia. Variation in benthic community response between sampling locations was attributed primarily to differences in effluent volume, with effluent quality and receiving water hydrodynamics playing secondary roles. The results of this study will help to inform the development of northern specific treatment performance standards which will aid in prioritizing community wastewater system upgrades in arctic communities.