Source Water Protection in Canada is regulated primarily by provincial governments, leading to a variety of approaches for characterizing threats to drinking water. This paper compares the key elements of vulnerability and threat assessments for microbial contaminants for two Canadian provinces. Drinking water intakes of two municipalities in Quebec and Ontario, Canada, located on opposite sides of a large transboundary river impacted by Combined Sewer Overflow (CSO) discharges were used as a case study to evaluate the two provincial approaches. Québec’s vulnerability classification for microbial contaminants is data driven based on regulatory monitoring (concentrations of Escherichia coli) at the drinking water intake) while that of Ontario’s is model driven and dependent on the physical and hydraulic characteristics of zones around an intake. To establish a quantitative criterion to compare these two threat assessment frameworks, the impacts of a series of CSO events upstream of the drinking water intakes were simulated using a calibrated hydrodynamic and water quality model. Corresponding enteric pathogen concentrations in the intakes were estimated and used as input for Quantitative Microbial Risk Assessment (QMRA) to calculate treatment requirement levels to meet human health targets. Unlike Ontario’s threat assessment approach, Quebec’s approach provides an opportunity to investigate the effectiveness of risk reduction strategies such as an adjustment of the frequency of CSO events or corrective actions to improve treatment. Considering the influence of CSO events on log removal requirements to remain compliant with human health targets permitted the differentiation of CSO risk levels for threat prioritization.