The variance analysis of fishery water quality data of five lakes from 2001 to 2011 (except 2004) was performed to compare the difference of the monitoring indicators among the five above-mentioned lakes in Jiangsu Province. And TOPSIS method was employed to give comprehensive comparison of water quality of the five lakes. The results indicated that the difference of 14 major water quality indicators was very significant among lakes except copper. In addition, transparency, total nitrogen, total phosphorus had very significant difference among stations for each lake; pH, chemical oxygen demand, oil, total phosphorus, lead, cadmium, mercury had significant or very significant difference among years for each station. The TOPSIS results showed that the fishery water quality of Gaobaoshaobo Lake was the best, and Luoma Lake was just second to it, followed by Hongze Lake, Taihu Lake and Gehu Lake. In combination with the geographic position of each lake, it showed that fishery water quality of the five investigated lakes was basically increasingly better from the south to the north in Jiangsu Province, and the trend revealed high association with the developed industrial economy.