Populations in Arctic Canada are strongly connected to, and draw sustenance from, the physical environment. Recreation and food harvesting locations, however, may be impacted by the basic wastewater treatment and disposal processes used in the region. Within these mixed socio-ecological systems, people may unknowingly be exposed to wastewater pathogens, either by direct contact or indirectly through activities resulting in exposure to contaminated locally harvested food. The objectives of this research are to estimate microbial health risks attributable to wastewater effluent exposure in Arctic Canada and evaluate potential mitigation options. A participatory quantitative microbial risk assessment (QMRA) approach was used. Specifically, community knowledge and information describing human activity patterns in wastewater-impacted environments was used with microbial water quality data to model a range of exposure scenarios and risk mitigation options. In several exposure scenario results, estimated individual annual risk of acute gastrointestinal illness exceeds a proposed tolerable target of 10-3. These scenarios include shore recreation and consumption of shellfish harvested near primary mechanical treatment plants at low tide, as well as travel in wetland portions of passive treatment sites during spring freshet. These results suggest that wastewater effluent exposures may be contributing to gastrointestinal illness in some Arctic communities. Mitigation strategies, including improved treatment and interventions aimed at deterring access to disposal areas reduce risk estimates across scenarios to varying degrees. Overall, well-designed passive systems appear to be the most effective wastewater treatment option for Arctic Canada in terms of limiting and managing associated microbial health risks. This research demonstrates a novel application of QMRA and provides science-based evidence to support public health, water, and sanitation decisions and investment in Arctic regions. All rights reserved, Elsevier.