The variations of phytoplankton functional groups and their correlation with environmental factors, as well as the applicability of phytoplankton functional groups to serve as biological water quality indicator in the Pearl River, South China, were studied in the present study. A total of 96 samples were collected and divided into 21 functional groups from September 2016 to July 2017. The phytoplankton functional groups P and G were dominant during the investigation, and their biomass contributing was ranged 0.06 to 89.07%, the average 30.73%, and ranged 1.47 to 62.40%, the average 9.33% of the total biomass, respectively. The results showed environmental estrogens—BPA (bisphenol A), E2 (17β-estradiol), E1 (estrone), 4-t-OP (4-tert-octylphenol), 4-NP (nonylphenol), TCS (triclosan), and TCC (triclocarban)—in the Pearl River were significantly different, and with average values of 269.30 ng L?1, 2.76 ng L?1, 4.24 ng L?1, 53.68 ng L?1, 952.72 ng L?1, 16.79 ng L?1, and 8.61 ng L?1, respectively. This was likely responsible for the differences in the phytoplankton functional groups. We observed positive correlations between P and A, and G and J. Functional groups P biomass decreased significantly with functional groups LM increased, and functional groups M and J with X2. We found positive correlations between functional group G and concentrations of E1 and TCC; functional group A and total nitrogen (TN), 4-NP, 4-t-OP, and E2; functional groups LM and L1 and total suspended particles, BPA, and TCS; and functional group G and negative total phosphorus (TP), pH, and TCS. The study showed that TN, TP, and the environmental estrogens in the aquatic ecosystems were correlation with phytoplankton functional groups type, and affected the ecological balance in aquatic environments.