Soil salinity in the southern region of Errachidia represents a major environmental challenge, particularly in arid environments where freshwater resources are scarce. This study aims to characterize the interactions between local lithology and experimental agricultural practices to assess the impact of saline irrigation on soil quality. Advanced geophysical methods, combining Very Low Frequency Electromagnetic (VLF-EM) and Electrical Resistivity Tomography (ERT), were applied at the Ain El Atti experimental site to map geological structures and analyze the distribution of salinity. The results revealed a highly conductive and relatively homogeneous subsurface. A NW-SE oriented fracture anomaly (with current density varying between 4 and 10%) in the SW part of the study area, identified through three-dimensional analysis, plays a key role in groundwater drainage and circulation, thereby influencing the spatial distribution of salinity. The resistivity pseudo-sections confirmed these findings, showing slightly resistive values (>100 Ohm-m) at depths of 10–15 meters, associated with alluvial and conglomeratic deposits. In contrast, deeper horizons exhibited high conductivity, attributed to marls and water-saturated sands, indicating significant salinity levels. These results, influenced by hydrogeological variability and irrigation practices, highlight the need for complementary hydrochemical and hydrogeological analyses. Nevertheless, this study provides crucial insights for soil and water management in arid regions. Identifying drainage structures could help optimize irrigation strategies and reduce soil degradation. The combined VLF-EM and ERT approach enhances the understanding of salinization processes and offers valuable perspectives for similar studies in other environmental contexts.