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This study focuses on identifying potential preferential groundwater flow paths beneath Lake Iseo using waterborne geophysical methods and groundwater modeling. The FloaTEM system was used to collect high-resolution subsurface data across 180 km in Lake Iseo and 20 km in nearby wetlands. The collected EM data were processed and inverted using advanced tools (EEMstudio and EEMverter) to produce 3D resistivity models of the southern shore of the Iseo Lake. Bathymetry data were integrated into the inversion process to improve accuracy by breaking constraints at the lake bottom surface. A resistivity threshold was used to identify areas potentially composed of permeable moraine sediments—indicative of preferential flow paths where groundwater exchange is most likely. These geophysical results were then used to inform a MODFLOW 6 groundwater flow model, implemented with Flopy. This model simulates how water might move from the lake to the surrounding aquifers and estimates the travel time of water particles.