We present a novel method to estimate the hydraulic and storage properties of a heterogeneous aquifer system using pilot-point-based hydraulic tomography (HT) inversion in conjunction with a geophysical a priori model. The a priori model involved a soil stratification obtained by combining electrical resistivity tomography inversion and field data from hydrogeological experiments. Pilot-point densities were assigned according to the stratification, which also constrained aquifer parameters during HT inversion. The forward groundwater flow model, HydroGeoSphere, was supplied to the parameter-estimation tool, PEST, to perform HT inversion. The performance of our method was evaluated on a hypothetical, two-dimensional, multi-layered, granitic aquifer system representative of those commonly occurring in the Kandi region in Telangana. Inversion results were compared using two commonly adopted methods of modeling parameter-heterogeneity: (1) using piece-wise zones of property values obtained from geostatistical interpolation of local-scale estimates; and (2) HT inversion starting from a homogeneous parameter field with a uniform distribution of pilot-points. Performances of the inverted models were evaluated by conducting independent pumping tests and statistical analyses (using a Taylor diagram) of the model-to-measurement discrepancies in drawdowns. Our results showed that using the aforementioned geophysical a priori model could improve the parameter-estimation process. © 2020 National Ground Water Association