With the rapid development of Chinese urbanization in the 21st century, urban diseases become more serious, mainly manifested in water environmental pollution, urban flooding, water shortage, and deterioration of water ecology. It is necessary to establish a modern rainwater management system, scientifically solve the problem of excess urban rainwater and to improve water environment quality. Improvement of water environment quality is conducive to the ecological function of a sponge city. Sponge city construction has contributed to control non-point source pollution. Sponge systems cause the stagnation and purification of rainwater runoff, which is an important guarantee for water environment quality. This monograph summarizes theories and practices of the integrated water environment treatment in Chongqing, a typical representative mountainous city in the Three Gorges Reservoir Region. Based on the mountainous terrain and unique water environment characteristics in the Three Gorges Reservoir Region, the monograph analyzes measures and difficulties in the basin water environment integrated treatment. Moreover, the monograph makes suggestions for risk management amid drainage systems during the COVID-19 epidemic.