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This study introduces a petrophysical joint inversion (PJI) framework integrating seismic refraction tomography (SRT), electrical resistivity tomography (ERT), and time-domain induced polarization (TDIP) to quantitatively characterize coastal aquifers. Two approaches are tested: a direct post-inversion transformation (N3PM) for rapid petrophysical estimation, and a full PJI method that inverts volumetric fractions of rock, water, and air, along with normalized chargeability. Field applications in two sites within the Pontina Plain (Central Italy) demonstrate the framework’s effectiveness under different geological and salinity conditions. While N3PM provides a quick screening when reliable prior knowledge exists, it suffers from physical inconsistencies in more complex settings. In contrast, the full PJI delivers robust results, accurately reconstructing water table levels, porosity distributions, and saline intrusion patterns. The inclusion of TDIP enhances resolution in detecting fine-grained sediments. This integrated geophysical–petrophysical approach offers a powerful non-invasive tool for coastal aquifer management, enabling high-resolution imaging and improved risk assessment.