Remediation of sites polluted by hazardous chemicals such as dense non-aqueous phase liquids (DNAPLs) represents an important environmental problem due to the large scale threat these releases pose to water supplies throughout the world. Successful cleanup and restoration relies on methods to characterize the source zone structure prior to remediation and subsequently to monitor the corresponding dissolved chemical levels. This paper develops and implements a new model-based approach to DNAPL source zone characterization based on the joint inversion of hydrological and geophysical data. To model the interaction of groundwater with the contaminant source zone, a fully three dimensional (3D) flow and transport model is used to provide the downstream contaminant concentrations associated to the source zone saturation distribution. As the geophysical modality we utilize electrical resistance tomography (ERT) where electric potential measurements related to the electrical properties of the medium are obtained cross gradient to the water flow direction. The inversion technique is based on the parametric level set method (PaLS) which provides for the recovery of the geometric profiles of the low and high saturation regions (corresponding to the ganglia and the pooling regions) and low order characterizations of the spatial variability within each region. The performance of our proposed algorithm is examined and discussed through the reconstruction of some challenging source zone architectures. © 2012 IEEE.