There is increasing public concern about the salinization of their groundwater due to rapid urban sprawl resulting in an increase in road salt use as de-icing and anti-icing agents on roads and parking lots within the water supply wells’ capture zones. Like many other communities in southern Ontario that rely on groundwater, the City of Guelph and its suburban communities are experiencing an increasing trend in chloride concentrations in a number of their bedrock groundwater supply wells. A few of these wells have already or soon are expected to exceed the Ontario Drinking Water Quality Standards for sodium and chloride. This study aims to characterize the hydrogeology of a complex multilayered aquifer-aquitard sequence to develop a better identification and risk assessment methodology for the salt vulnerability of these systems. Continuously cored holes combined with hydrogeophysical logging were used to inform the placement of multi-level monitoring ports in the Silurian dolostone sequence for monitoring physical and chemical properties within the semi-confined aquifer. Results show evidence for higher salinity zones underlying shallower zones of lower salinity suggesting lateral flow from distal recharge areas within the 3D flow system. This study is complemented by the City of Guelph’s groundwater chemistry and the Ontario Geological Survey’s monitoring datasets. This study provides essential insights into the spatiotemporal complexity of non-point source contaminants in fractured bedrock aquifers. This study will provide a more accurate method for mapping the salt-vulnerable areas for municipalities to help with salt management plans and better protect precious groundwater resources.