This article analyzes the appropriate types of water rights systems for different regions with varying water resource conditions in China. The most appropriate water rights systems for various zones were determined by comparing the value of influencing factors with corresponding thresholds in China’s second-class zones of water resources. It is shown that a riparian rights system under water withdrawals permission could be adopted in most regions of southern China. For most northern Chinese regions, the quantity proportional water rights systems should be adopted and further improved. In contrast to the implementation of a single quantity proportional water rights system, this paper innovatively proposes a zoning scheme for China’s water rights system. The appropriate type of water rights system can be identified according to the region’s specific water resource conditions. It can provide a scientific reference for the reform of water rights systems in China and other countries or regions.