As coastal hazards such as storm surge, erosion, and flooding increasingly threaten coastal communities, there is a growing need to understand their impacts on key infrastructure. There are currently over one million onsite wastewater treatment systems (OWTS) in Ontario with many of them serving coastal communities along the Great Lakes. Climate change poses multifaceted challenges to the proper functioning of OWTSs located close to inland coastal waters such as the Great Lakes due to factors including lake level changes, shoreline recession and coastal flooding. Improperly functioning systems pose public health risk as well as ecosystem health challenges due to increased pollutant loads to inland waters. Through field investigations, historical data analysis, and predictive modeling techniques, this study explores the potential impacts of climate change induced stressors on the functioning of OWTSs located near the Great Lakes. This study first provides field-based evidence that shoreline recession associated with record high lake water levels accelerated and increased inputs of nutrients from a large OWTS to Lake Huron. Second, the study uses geospatial approaches to explore the potential impact of greater coastal flooding and coastal erosion on the vulnerability of OWTSs to fail (or underperform) and potential implications for pollutant inputs to the Great Lakes. The study provides new insights needed to inform management and policy decisions (e.g., OWTS installation and maintenance guidelines), develops adaptation and mitigation strategies, and designs currently overlooked belowground infrastructure to limit future subsurface and surface water pollution, and improves the resilience of coastal communities to a changing climate.