Xili reservoir is one of the most important drinking water reservoirs in southeast China, ensuring the safety of water supply in Shenzhen city. Understanding the water balance in the reservoir system under climate change and human activities is essential for making optimal water use planning. To assess the water balance of the Xili reservoir system, the water isotope characteristics in rainfall, reservoir water, groundwater, soil, and plant were investigated. The variation of isotope composition in rainfall, reservoir water, and groundwater indicates the different recharging and mixing water sources. A mathematical mass-balance model was established to evaluate the water budget in the Xili reservoir. Roughly 35% of total incoming water was consumed by evaporation, which reminds managers to pay more attention to making scientific planning.