This research analyzes the potential effects of climate change and land use dynamics on groundwater in highly productive agricultural regions dependent on water imports and groundwater regulation. Before focusing on the research topic, solving a series of conceptual, operational, and computational challenges, such as having reliable, integrable, and fast models, was necessary. So, in the first part of the research, we evaluate the performance of three emulators of the sophisticated hydrology model known as the Fine Grid California Central Valley Groundwater-Surface Water Simulation Model (C2VSimFG) to estimate how climate and agriculture affect groundwater levels. Once the best emulator was identified, we assessed the hypothesis that groundwater levels in the Greater Kern County Region would exhibit a more rapid decline with projected climate change scenarios compared to a historical climate resembling 1995 and 2015. Finally, we focus on determining economically and environmentally optimal operational policies for the Shafter-Wasco irrigation district by considering the conjunctive water use approach and identifying the best policies through Bayesian Optimization Programming. The findings suggest groundwater levels are likely to decline unless agricultural water demand is reduced and recharge is increased, with climate scenarios exacerbating this decline compared to historical conditions. Our findings underscore the balance between profit and aquifer recovery, indicating farmers' need to curtail profits to achieve groundwater sustainability. Ultimately, our method can potentially integrate water and agricultural systems facing various uncertainties, providing valuable insights into optimal operational policies and tradeoffs.