Understanding the factors controlling groundwater mineralization is essential for the sustainable management of water resources in semi-arid environments. This study investigates the hydrogeochemical functioning of the Chemora Plain aquifer (northeastern Algeria), where a Cretaceous structural ridge divides the alluvial basin into northern and southern hydrogeological compartments. A multidisciplinary dataset combining major-ion hydrochemistry, water hardness, mineral saturation indices, stable isotopes (δ¹⁸O and δ²H), and principal component analysis (PCA) was used to test the hydrogeochemical significance of this structural organization. Electrical conductivity, hardness and major-ion distributions reveal differentiated groundwater evolution between the southern and northern compartments, while comparable EC values near the structural boundary indicate that the compartments are not completely isolated. Saturation indices show near-equilibrium conditions for carbonate minerals and persistent undersaturation with respect to gypsum, anhydrite and halite, supporting continued water–rock interaction and a potential contribution of evaporite dissolution to mineralization. Stable isotope compositions (δ¹⁸O = −8.96 to −5.89‰; δ²H = −54.98 to −39.10‰; d-excess = 7–17‰) indicate a predominantly meteoric recharge source with limited isotopic modification. PCA further identifies distinct hydrochemical associations for the northern and southern sectors, while shared variables indicate partial hydraulic connectivity. The integrated evidence supports a conceptual model in which the Fedjoudj–Bouarif Cretaceous ridge acts as a major structural threshold, whereas the western breach permits localized hydraulic exchange. The main contribution of this study is therefore the demonstration of a structurally controlled hydrogeochemical evolution in the Chemora aquifer through the convergence of independent geological, hydrochemical, isotopic and statistical evidence.