The present study employs a multidisciplinary approach to investigate lineaments as surface expressions of deep crustal structures within the Bou Arada-El Aroussa (BAEA) plain in the Northern Atlasic domain of Tunisia. The research aims to elucidate the structural controls on aquifer hydrodynamics, specifically examining the role of faults and fractures in enhancing permeability and facilitating groundwater recharge. Remote sensing data (Landsat 8 OLI/TIRS) processed using Principal Component Analysis, band ratios, and composite imaging, were integrated with geological maps in a GIS environment. This enabled the extraction and spatial analysis of lineaments, yielding 747-839 features automatically and 730 from manual digitization. Machine learning techniques (Scikit-learn, SciPy) were applied to classify the complete lineament dataset into three distinct clusters based on orientation and length, revealing zones of high fracture density associated with major tectonic structures and fault reactivation. The analysis demonstrates that groundwater flow directions and aquifer recharge are predominantly influenced by NW-SE, E-W, and N-S oriented lineaments. A high density of NW-SE and N-S lineaments between Koudiet Sidi Barka and Jebel Rihane promotes rapid infiltration, critically recharging the BAEA aquifer. In contrast, E-W trending lineaments within the Bou Arada trough function as hydraulic conductive barriers, compartmentalizing the flow system. These interpretations are corroborated by piezometric data, which identify primary recharge areas at the foot of Jebel Rihane, Koudiet Sidi Baka, Jebel Bessioud, and Jebel Er Rmil. The findings provide a robust framework for understanding structural controls on groundwater resources and offer critical insights for the sustainable management of this fractured aquifer system under semi-arid conditions.