In order to reveal the reasons of the dramatic decline of wild Chinese alligator population, an investigation on its habitat status was made across the National Natural Conservation Regions of Chinese alligator in south Anhui Province from 2002 to 2003. Water samples from 21 sites were collected, and their heavy metals (Cu, Zn, Cd and Pb) content and pH value were measured. The results showed that the pH value was 7.84 +/- 0.62, with no significant difference between the waters with and without Chinese alligator, but with significant difference (P< 0.01) among 3 Chinese alligator habitats. In the waters with and without Chinese alligator, no significant difference was observed in the contents of test metals except Pb. The possible pollution source of Pb in wild Chinese alligator habitat was analyzed, which could provide reference for Chinese alligator conservation.