Water ecological security is a crucial element of national ecological civilization construction. Based on the DPSIR model, this study constructed an evaluation index system of China’s water ecological security and applied the comprehensive index method and obstacle degree model to evaluate water ecological security and diagnose obstacle factors in China’s 31 provinces from 2012 to 2022. The results show that: (1) China’s water ecological security situation is severe, with an overall fluctuating downward trend. The performance of each subsystem of water ecological security varies. (2) The level of water ecological security in China’s eight economic regions differs significantly, showing a spatial distribution pattern of stepwise decline from east to west. The eastern coast performs better than the national average, while the situation in the southwestern, northeastern, and northwestern regions is critical. (3) The main obstacles to China’s water ecological security lie in the impact, status, and response subsystems, reflected in the poor condition of water environment, intensified impact of water problems, and insufficient governance response. (4) Water scarcity, groundwater over-exploitation, inadequate water pollution control, and insufficient water supply capacity are common issues across China’s eight economic regions, but the focus varies regionally. Accordingly, recommendations are made to promote the steady improvement of China’s water ecological security.