Zhejiang area of Taihu Basin is affected by human factors such as industrial, urban wastewater and farmland surface runoff. Pollution problems are becoming more and more serious. Based on the data of hydrological survey and water quality monitoring in 2013, inbound and outbound water quantity and spatial-temporal distribution of water quality indexes such as permanganate index (COD_Mn), ammonia nitrogen (NH₃-N), total nitrogen (TN) and total phosphorus (TP) in Zhejiang area of Taihu Basin were analyzed. The results showed that the inbound and outbound water quantity in Zhejiang area of Taihu Basin in 2013 was mainly outbound. The primary pollutant in the entry-exit section is TN. The average concentration is in the V-inferior V level in all entry-exit sections. The average concentrations of COD_Mn, NH₃-N, and TP generally reach the Ⅱ-Ⅲ standard. The outbound and inbound fluxes of the four pollutants are mainly outbound. The northern part of the study area is the main inbound section of pollutants, and the eastern part is the main outbound section of pollutants. The net outbound water quantity is the key factor affecting the net outbound flux of pollutants, and the water quality of the entry-exit section is the main factor affecting the net outbound flux. The key to reducing water pollution in Zhejiang area of Taihu Basin is controlling agricultural non-point source pollution and discharging industrial wastewater and urban domestic sewage after reaching the standard, which is the main measure of water pollution control and treatment in Taihu Basin.