Wastewater management in Canadian Arctic communities is influenced by several geographical factors including climate, remoteness, population size, and local food-harvesting practices. Most communities use trucked collection services and basic treatment systems, which are capable of only low-level pathogen removal. These systems are typically reliant solely on natural environmental processes for treatment and make use of existing lagoons, wetlands, and bays. They are operated in a manner such that partially treated wastewater still containing potentially hazardous microorganisms is released into the terrestrial and aquatic environment at random times. Northern communities rely heavily on their local surroundings as a source of food, drinking water, and recreation, thus creating the possibility of human exposure to wastewater effluent. Human exposure to microbial hazards present in municipal wastewater can lead to acute gastrointestinal illness or more severe disease. Although estimating the actual disease burdens associated with wastewater exposures in Arctic communities is challenging, waterborne- and sanitation-related illness is believed to be comparatively higher than in other parts of Canada. This review offers a conceptual framework and evaluation of current knowledge to enable the first microbial risk assessment of exposure scenarios associated with food-harvesting and recreational activities in Arctic communities, where simplified wastewater systems are being operated.