Toxic organic contaminants in groundwater are pervasive at many industrial sites worldwide. These contaminants, such as chlorinated solvents, often appear as dense non-aqueous phase liquids (DNAPLs). To design efficient remediation strategies, detailed characterization of DNAPL Source Zone Architecture (SZA) is required. Since invasive borehole-based investigations suffer from limited spatial coverage, a non-intrusive geophysical method, direct current (DC) resistivity, has been applied to image the DNAPL distribution; however, in clay-sand environments, the ability of DC resistivity for DNAPLs imaging is limited since it cannot separate between DNAPLs and surrounding clay-sand soils. Moreover, the simplified parameterization of conventional inversion approaches cannot preserve physically realistic patterns of SZAs, and tends to smooth out any sharp spatial variations. In this paper, the induced polarization (IP) technique is combined with DC resistivity (DCIP) to provide plausible DNAPL characterization in clay-sand environments. Using petrophysical models, the DCIP data is utilized to provide tomograms of the DNAPL saturation (SN) and hydraulic conductivity (K). The DCIP-estimated K/SN tomograms are then integrated with borehole measurements in a deep learning-based joint inversion framework to accurately parameterize the highly irregular SZA and provide a refined DNAPL image. To evaluate the performance of the proposed approach, we conducted numerical experiments in a heterogeneous clay-sand aquifer with a complex SZA. Results demonstrate the standalone DC resistivity method fails to infer the DNAPL in complex clay-sand environments. In contrast, the combined DCIP technique provides the necessary information to reconstruct the large-scale features of K/SN fields, while integrating DCIP data with sparse but accurate borehole data results in a high resolution characterization of the SZA.