Contamination of perfluoroalkyl acids (PFAAs) is ubiquitously detected in various environments. However, their potential effects on microbial communities remain largely unknown. In this study, surface seawater of the Pearl River Delta (PRD) is sampled to measure PFAA concentrations and profile the structure of free-living microbial community. Total PFAAs concentrations range from 131 to 1563 pg L-1 in surface seawater. PFOS (16-470 pg L-1), PFOA (27-272 pg L-1), PFHpA (18-201 pg L-1) and PFBA (25-152 pg L-1) are the major homologues, indicating continued industrial application or release of PFOS and a gradual shift towards using shorter-chain PFAAs. Concentrations of PFAAs from this recent cruise are much lower than previous reports, which may be due to the effective management of PFAA usage around PRD region. In addition, the microbial community in PRD surface seawater is predominantly colonized by the Proteobacteria phylum (27.2 to 61.5%) and the Synechococcus genus (5.6 to 38.6%). The structure of the microbial communities varies among stations, mainly resulting from different abundances of Synechococcus, Prochlorococcus and Nitrosopumilus. Geochemical parameters (e.g., nutrients and salinity) and phytoplankton are significantly associated with the microbial community dynamics in surface seawater. In the interactive network of microbiota, a subset of bacteria (i.e., Fluviicola, Nitrosopumilus, Limnohabitans, Sediminibacterium, C39 and Polynucleobacter) shows significantly positive correlations with PFAAs (R > 0.6; P < 0.001). Overall, this study gives a timely monitoring of PFAA pollution around PRD area. Shift in environmental microbiota by geochemical factors and phytoplankton is also observed, which may affect biogeochemical cycling.