First Nations communities in Canada have a documented history of sub-standard water quality. While efforts have been made to address drinking water quality, little has been done to address longstanding challenges in wastewater systems. This study developed a hazard identification checklist using a sanitation safety plan (SSP) framework to characterize potential hazards in 29 First Nations wastewater systems in Atlantic Canada. System types included in this study included centralized, decentralized, and municipal transfer agreements (MTAs). Using past system assessment reports, potential hazardous events were evaluated along the sanitation chain to assess risk within systems. Overall, 69% of hazardous events had an unknown level of risk while 7% were high-risk. This research found that decentralized systems and MTAs have poorly characterized risk due to a lack of documentation and communication. The presence of significant knowledge deficits and high-risk hazards in centralized systems cause risk propagation and accumulation along the sanitation chain, resulting in potential effluent quality concerns. This desktop study demonstrates that an SSP approach offers an alternative assessment process to the regulatory approach currently being used by proposing an enhanced systemic understanding of risk that can inform management practices and integrate the plurality of stakeholders involved in these systems.