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To evaluate the impacts of wastewater from upper reaches, characteristics of microbial community were investigated using (PFU) method at four sampling stations in Baiyangdian Lake. At the same time, water sampling from these stations was conducted and five chemical parameters, including TP, TN, CODcr, NH4+-N and BOD5, were analyzed. Comprehensive chemical pollution index (PB) was also calculated based on the five chemical parameters. A total of 172 protozoan species were indentified, including 44 species of Phytomastigophoreas, 17 species of Zoomastigophoras, 31species of Sarcodinas, and 80 species of Ciliates. The results showed that the parameters of PFU microbial communities, including number of protozoan species, diversity index (DI) and heterotrophic index (HI), can objectively reflect the degree of water pollution. The results also indicated that external pollution source, especially wastewater from Baoding City, adversely affected the water quality of Baiyangdian Lake.