The water quality of six different aquaculture systems in freshwater ponds was investigated in Jiangsu Province of China in order to elucidate the influence of different aquaculture systems on water quality. The six aquaculture systems involved in this study were: monoculture of shrimps and crabs, polyculture of shrimps and crabs, polyculture of fish and crabs, polyculture of crabs and various types of fish, and polyculture of different types of fish. The results showed that the water temperature of those six aquaculture ponds decreased from south to north and that all DO values were higher than standard value of Grade I water for Surface Water Quality Standards in China (GB 3838-2002) (DO≥7.5 mg /L). For all systems, the pH values ranged between 7.36 and 8.54, and nitrite concentrations were below China’s aquaculture water standard value (0.12 mg/L); however, all ammonia concentrations were higher than the national standard (0.20 mg/L). In comparison, water quality from the monoculture of shrimp and crabs was much better than that from other aquaculture combinations. Polyculture of different types of fish showed the highest nitrite (0.030 mg/L) and ammonia (0.86 mg/L) concentrations among the six aquaculture systems. In general, the pond aquaculture in china is in a rough management state, and strict and reasonable control of the aquaculture is urgently needed. So it is highly recommended that we establish an ecological and healthy aquaculture mode suitable for sustainable development of the aquaculture industry in China.