One-third of the global population depends on groundwater for drinking, which is an even larger proportion for arid regions. The integration of isotopic and geophysical applications has been very useful in understanding the process of groundwater recharge. The aim of this study is to define a conceptual model that describes groundwater functions within an aquifer located in a semi-arid region by identifying recharge patterns based on the isotopic characteristics of: Rainfall, surface water, shallow and deep groundwater, and incorporating regional geophysical data. We demonstrated that rainfall was affected by sub-cloud evaporation and altitude. Shallow and deep modern groundwater samples were clustered and exhibited similar evolution from rainfall. However, different groups recharged from different precipitation sources compared to the local one. In the current study, we analyzed the isotopic evolution of deep groundwater over a 10-year period, which was mainly affected by the incorporation of different flows with different isotopic signatures and the hydrodynamics of the area. We performed two geoelectrical sections in the study area to improve the understanding of the hydrogeological setting and water movement patterns. The new conceptual model should help stakeholders in the context of water management policies for the study area.