Results show increasing calcium from enhanced water-rock interaction due to increased precipitation, and declining salinity, indicating dilution. These findings align with climatic shifts (e.g., 9% precipitation rise, 81% snowfall reduction). Concurrently, nitrate and chloride concentrations decreased, linked to reduced paddy cultivation and improved wastewater management. Our findings reveal that climate-driven recharge has emerged as the dominant factor shaping the aquifer’s chemistry, surpassing land-use influences and enhancing dilution of waters. This dilution trend poses risks of nutrient limitation, coastal acidification, and reduced primary productivity in adjacent marine ecosystems. These insights underscore the imperative of integrating climatic and land-use considerations into adaptive nutrient management strategies for global groundwater and coastal ecosystem health.