Abstract: To further protect the water eco-environmental quality in Chengdu-Chongqing area and build a strong ecological security barrier in the upper reaches of the Yangtze River, the problems existing in the water environmental protection of small and medium-sized rivers were analyzed based on the pollution characteristics of water quality in Chengdu-Chongqing area. Countermeasures were put forward to strengthen the water environmental protection of small and medium-sized rivers. The results showed that: 1) The water quality in Chengdu-Chongqing area was gradually improving. The water pollution was mainly concentrated in small and medium-sized rivers, especially in the transboundary rivers, where the water quality exceeded the standard frequently. The water quality pollution of small and medium-sized rivers in the region mainly appeared from February to June, indicating that the regional water quality was jointly affected by the point source pollution and the non-point source pollutants which were flowed into the river with the initial rainwater. 2) The main reasons for the prominent water quality pollution of small and medium-sized rivers in Chengdu-Chongqing area included: the insufficient ecological flow caused by uneven distribution of water resources and high-intensity development, the high domestic source pollution caused by urban population agglomeration, the long-term high pollution load caused by the difficulty in non-point source pollution control, and the difficulty in water quality protection of transboundary rivers caused by incomplete mechanism in upstream and downstream joint prevention and control. 3) It was suggested to strengthen the ecological flow guarantee of small and medium-sized rivers, pay close attention to the plant and network to promote the quality and efficiency of urban domestic sewage treatment, take multiple measures to improve the prevention and control level of agricultural and rural non-point source pollution, and comprehensively promote the level of water environment management in the basin.