After decades striving of water pollution control，the water quality has been improved significantly in Shanghai. With the rapid socio-economic development，further improvement of water quality has become more difficult. The surface runoff and discharge to river of drainage pump stations in the central city area and agricultural non-point source pollutions in rural area are the main threads to the water environment in Shanghai. The control level and management capacity of the urban water environment has been put forward higher requirements. Based on summarizing the achievements and existing problems of water pollution control in Shanghai，this paper discusses the highlights of the water pollution control，such as urban non-point source pollutions，agricultural non-point source pollutions and water environment improvements of the water sources. The study suggested that Shanghai should strengthen the analysis of water environment capacity and promote the multiple planning integration of water environment related fields，innovate the water environment management systems to improve the management efficiency，and establish the water quality target responsibility examination system to strengthen the ability of water environment management of the town and village level governments.