This study investigates an aquifer system in Guelph, Ontario, where trace concentrations of trichloroethylene have been detected in a municipal supply well since the mid-1990s. Using high-resolution multi-depth monitoring, four boreholes were drilled radially around the supply well (1 km2 area, ~70m deep), intersecting flow paths between the well and suspected threats. Of the four boreholes, one location was selected as a method calibration borehole where a suite of geophysical and hydrophysical datasets were collected, following the discrete fracture network–matrix field approach (Parker et al. 2012). Incorporating temporal variation, 13 hydrogeologic units with distinct geometries and hydrogeologic properties were identified and evaluated against existing regional conceptual site models. The improved understanding of subsurface heterogeneity, and the position and thickness of aquitard units around the supply well, will be used to update existing numerical flow models, evaluate risks to water resources and improve strategies for long-term urban aquifer management.