Although most water balance models include groundwater components within their structure, the involvement of the sub-surface processes is less well represented as compared to the surface processes. Not only the interaction between surface water and groundwater is important, but the interchanging cross-aquifer flow is also of great significance to consider. Especially in areas where the hydrogeological setting consists of several layers, and a considerable amount of groundwater is consistently abstracted from various depths due to population growth and climate change, the flow occurred between unconfined and confined groundwater layers could influence the groundwater table fluctuation. To a greater extent, it could imply changes to the overall basin-scale water balance. Yet to be mentioned, it is also important to be able to adapt under data-scarce circumstances. In principle, this study is aimed to quantify the influence of the sub-surface flow in particular to basin water balance considering anthropogenic and climatic drivers, starting from assessing the current water balance situation and the uncertainties, constructing groundwater model based on the assessment, evaluating its performance on filling the gap of information on water balance components, and finally, providing research-based recommendations to improve groundwater management.