In order to resolve the water problems, including water resources, water environment, water ecology and water disaster in China, a logic framework of 36 sub-systems was built. This logic framework was based on the ecological carrying capacity theory which contained ecological elastic capability, resources carrying capacity and environmental carrying capacity, and the basic characteristics of water ecological civilization was also considered. The system of water ecological civilization could be divided into four categories, including orderly management of water space, rational utilization and supervision of water resources, effective management of water environment and ecology, evaluation and assessment. Through statistic analysis of the sub-systems for each category, basic problems and solutions were proposed. First of all, there were some problems in the process of pilot. Corresponding solutions should be made to accumulate experience and improve the sub-systems. Furthermore, some sub-systems in laws and regulations were too simple and they should be refined in the future. Last but not the least, some sub-systems contradicted with the present laws, regulations or systems. Before piloting, relevant laws, regulations or systems should be adjusted temporarily.