The water quality identification index method was used to evaluate and analyze the comprehensive water quality of the inflow, aquaculture tail water and the discharge water from aquaculture tail water treatment system in the freshwater aquafarm.Total solid suspended matter (TSS), organic matter (COD_Mn), total ammonia nitrogen (TAN), total nitrogen (TN) and total phosphorus (TP) were taken as single factor evaluation indexes and comprehensive evaluation indexes. The comprehensive water quality was evaluated and analyzed according to Environmental Quality Standard for Surface water(GB 3838-2002) or Requirement for Water Discharge from Freshwater Aquaculture Pond (SC/T 9101-2007). Research indicated that:TN was the main pollutant in the inflow of the aquafarm. TP and TSS were the key risk factors of pollutants in the ponds. Aquiculture tail water treatment system played an important role in the integrated water quality purification of aquiculture tail water. After the eastern pond tail water was treated by the aquiculture tail water treatment system (S1), the comprehensive water quality was improved (I_ΔX1.X2=13%), and the main pollutant TN was significantly improved (I_ΔX1.X2=23%). After the western pond tail water was treated by the aquiculture tail water treatment system (S2), the comprehensive water quality was slightly improved (I_ΔX1.X2=9%). The comprehensive water quality of the discharge water was equal to or better than that of the inflow in the aquafarm by aquaculture tail water treatment system to purify aquaculture tail water, and it met the first-level discharge standard of SC/T 9101-2007, and had no negative impact on the environment of adjacent natural waters, but also had a slight improvement effect.