The reservoir has a mixed influence on the water quality of Yangtze River. Due to its adjustment, the flow in drought period will increase, which will improve the water quality and relieve the invasion of saline tide in the river's mouth to East China Sea. On the other side, the sewage discharged into the River is more than 1.35 billion tons per year nowadays, which forms a heavy pollution of the water. With the rise of water level, the flow will slow down, which is unfavorable to the pollution. Therefore, the state has increased investment to control the pollution in this area.

According to the Gazette of Ecological and Environmental Monitoring published by the State Environmental Protection Administration of China in 2002, the water quality of the Yangtze in TGP area still kept not bad in 2002, most better than or at class III, though industrial wastes directly emitted to the River increased by 23.8% than in 2001, the environmental quality of the project areas kept good. Environmental monitoring in 2003 indicates that overall management of water quality in TGP area has obtained initial achievement, with a decrease ratio at class IV and increase at class II and III compared to the period before impoundment.