In semi-arid regions, groundwater is a vital water resource threatened by salinization and contamination. Geophysical and the physicochemical and isotopic compositions (delta O-18 and delta H-2) are investigated to determine the general geometrical characteristics of a closed basin and identify the origin and main evolutionary processes controlling the groundwater geochemistry and quality to provide reliable information for effective water management. The studied dominantly unconfined Mirandiba Basin lacks evaporitic (halite) deposits but contains comparatively higher chloride concentration, under the role of the semi-arid climate of NE Brazil. Geophysics unravels a shallow basin with a thickness lower than 400 m and a basement morphology suggesting a half-graben structure. Groundwater samples were classified into three groups: 1) cluster 1 samples correspond to more mineralized mixed cations-Cl to Na-Cl slightly acid waters, 2) cluster 2 samples correspond to less mineralized Na-Cl acid waters, and 3) cluster 3 samples correspond to neutral mixed cations-mixed anions waters. The isotopic signatures range from -4.95 to -3.16 parts per thousand and - 29.74 to -17.50 parts per thousand for delta O-18 and delta H-2, respectively, indicating that groundwater is derived from rainwater with some samples suggesting evaporation. The integrated techniques have shown that the main factors controlling groundwater chemistry evolution are related to 1) wetting/evaporation that induced millennial cyclic salt (mainly halite) accumulation and later dissolution and leaching during recharge periods, 2) rock weathering, 3) reverse ion exchange, and 4) anthropogenic nitrate contamination. The physicochemical parameters of similar to 90 % of groundwater samples are within the WHO guidelines, and similar to 92 % within the good and excellent water quality category for drinking purposes. Similarly, irrigation ion-based indices showed overall suitability for irrigation. The approach followed in this study is useful for recognize the main processes (natural and anthropogenic) operating in groundwater, and was used to build a conceptual hydrogeologic model, for establishing effective management strategies in aquifers in arid to semi-arid areas.