In the context of the reform of the ecological civilization system in the new era, water pollution control should take the balance between economic development and environmental protection into account. The trading of water pollution rights is a policy of controlling water pollution through economic measures, which can achieve the coordination and unification between them. In the 1980s, China began to explore water pollution rights trading system. In recent years, China has accelerated the pace of market construction and achieved some results. However, there are still some problems in the system of water pollution rights trading system in China.The position of pollution rights is not clearly defined in the law.There is no connection between local legislations.Administrative measures are too strong.And there is no effective supervision mechanism. These problems have seriously hindered the development of water pollution rights trading market in China. In order to promote the construction of water pollution rights market in China, it is necessary to perfect the legal system of water pollution rights trading from the following three aspects: clearly defining the related concepts of pollution rights and status in law; strengthening legislation work of cross administrative regions in the basin; establishing the supporting system of administration enforcement supervision and strengthening the public participation.