Per- and polyfluoroalkyl substances (PFAS) are widespread, highly persistent, and bio-accumulative compounds that are increasingly found in the sediments of aquatic systems. Given this accumulation and concerns regarding the environmental impacts of PFAS, their influence on sedimentary bacterial communities remains inadequately studied. Here, we investigated the concentrations of 17 PFAS in sediments from six urban lakes in Nanjing, China, and assessed their effects on the diversity, composition, potential interactions, and assembly mechanisms of sedimentary bacterial communities. Sediment concentrations of PFAS ranged from 4.70 to 5.28 ng·g dry weight. The high concentrations of the short-chain perfluorobutanesulfonic acid (PFBS) suggested its substitution for the long-chain perfluorooctanesulfonic acid (PFOS). As alternatives to long-chain PFAS, short-chain PFAS had similar effects on bacterial communities. The short-chain perfluoropentanoic acid (PFPeA) and the long-chain perfluorotridecanoic acid (PFTrDA) were the most important PFAS related to the ecological patterns of the co-occurrence network and may alter the composition of the sedimentary bacterial communities in the urban lakes. The Anaerolineaceae family represented as keystone bacteria within the PFAS-affected bacterial co-occurrence network. Deterministic processes (65.9 %), particularly homogeneous selection (63.2 %), were the dominant process driving bacterial community assembly. PFAS promoted the phylogenetic clustering and influenced the community dispersal capabilities to shape bacterial community assembly. This study provides a comprehensive analysis of PFAS distribution in sediments across six urban lakes in Nanjing and provides novel insights into the effects of PFAS on sedimentary bacterial communities. Further research is required to elucidate the mechanisms underlying the impacts of PFAS on microbial communities and to evaluate their broader ecological consequences.