An airborne electromagnetic (AEM) survey using the ResolveTM frequency-domain system was completed over a 50 km2 bedrock-groundwater-dependent region near Elora, Ontario, Canada. The effectiveness of this geophysical method to delineate lithostratigraphic units and characterize variations in Quaternary and bedrock physical properties such as mineralogy/clay content and aquifer characteristics was assessed using high-resolution continuous core, downhole geophysical logs, and surface electrical resistivity measurements. Several high-resolution logs were collected within and adjacent to a buried bedrock valley to characterize Quaternary and bedrock deposits. A statistical bootstrapping approach was used to establish the range in electrical conductivity most likely associated with clay, diamict, and sand/gravel units. The resulting statistical output was used to generate a 3D lithostratigraphic model of the Quaternary deposits restricted to the buried bedrock valley region. This study demonstrates the utility of combining geophysical and geological datasets through statistical analysis to map bedrock morphology and Quaternary infill architecture at scales relevant to municipal groundwater flow systems.