The escalation of groundwater withdrawal has been massive, particularly driven by population growth and changing climate factors. Further, groundwater over-abstraction from various aquifer depths and layers has triggered interaction between unconfined and confined groundwater, which magnitude of influence to basin water balance remains unknown. Despite the need to understand the sub-surface processes, however, such analysis is often demanding in data-scarce regions with gaps of hydrological components information. Therefore, this research is aimed to quantify these water-balance elements and its correlation with unconfined – confined groundwater interaction considering the associated driving factors, and to provide research-based recommendations to improve groundwater management.