Geological modeling has become a valuable tool for characterizing reservoir architecture. It is only possible with a fundamental conceptual model, which is, in turn, based on hypotheses about geological evolutionary processes. This study aims to develop the first 3D geological and hydrostratigraphic model of the Dakhla Basin in the southwestern Moroccan Sahara, addressing the challenges its complex lithology poses. Geological maps and borehole log-derived cross-sections were employed by the Groundwater Modeling System (GMS) to create a detailed 3D model, with a corresponding modeling workflow established. Finally, our findings classify the basin into ten geological and five stratigraphic units, revealing a monocline structure oriented east-west. Notably, the model identifies a deep aquifer within SU3 (Paleogene), primarily composed of fine to medium sand and sandstone, with an estimated volume of 1.71 × 10¹² m³, representing a vital water resource for the region. Additionally, the model uncovers east-to-west groundwater flow patterns and recharge areas in the northeast and eastern parts of the basin. These results provide new insights into the region’s geology and hydrostratigraphy, advancing research and practical applications in groundwater resource management.