The development of a three-dimensional (3D) hydrogeologic site model requires detailed knowledge of an area's hydrostratigraphy, information typically obtained from core logs, historical well records, outcrop mapping, and/or surface geophysics. Due to the high cost of drilling, a 3D model may rely on various statistical techniques to interpolate lithological boundaries between points located tens of kilometers or more apart. This situation can result in poorly constrained or simplified lithostratigraphic models, with under-sampled features such as karst and buried bedrock valleys. The non-invasive nature of airborne geophysical surveys combined with its dense sampling capability can fill critical data gaps. This study evaluates the capacity of a helicopter borne frequency-domain electromagnetic (FDEM) and residual magnetic survey using the Resolve™ system over a buried bedrock valley incised in a multi-layered dolostone aquifer within a complex glaciated environment in an urban/agricultural region of southern Ontario, Canada. The resulting airborne data was evaluated against two high-resolution ground-based electrical resistivity transects oriented orthogonal to the valley, alongside a published Quaternary geological model. A comparison between our local geophysically-based model and the regional geological model shows that the airborne electromagnetic surveys can markedly improve characterization of bedrock valley morphology and Quaternary sedimentary unit architecture that is comparable to that obtained using high-resolution surface-based electrical resistivity measurements with 10 m electrode spacing. The scale of heterogeneity that can be resolved by the airborne survey reveals the level of petrophysical variability that can be seen within the valley infill. Our study demonstrates the potential of airborne FDEM surveys in semi-urban agricultural environments where detailed characterization of Quaternary sediment architecture and bedrock topography is needed to inform 3D groundwater flow system variability.