Compared the Taihu Lake and Three Gorges reservoir from social economy and physical geography, evaluated the possibility of nonpoint source pollution (NPS pollution) in Three Gorges reservoir. The results showed that there are similarities in agricultural environment and genetic condition of nonpoint source pollution between Taihu Lake and Three Gorges reservoir. On the other hand, the sources of NPS pollutant in Three Gorges reservoir, such as sediment and nutrients, were abundance. So it can be extrapolated that Three Gorges reservoir had a great potential possibility of NPS pollution.