Emerging poly/perfluoroalkyl substances (PFASs) have been widely detected in the environment, but their bioaccumulation and biomagnification behaviors are not well understood. We collected surface water, sediment, and various aquatic organisms from Lake Taihu, China. Several emerging PFASs, such as fluorotelomer sulfonates (FTSs), hexafluoropropylene oxides (HFPOs), and chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) were frequently detected in water and sediment samples. The concentrations of HFPO trimer acid (HFPO-TA), 4,8-dioxa-3 H-per-fluorononanoate, and FTSs were remarkably higher than those reported previously, indicating that their application is increasing in Taihu Basin. These emerging PFASs displayed higher sediment/water partitioning coefficients (log K_oc) than the corresponding perfluoroalkyl acids (PFAAs) with the same perfluorinated carbon chain length. HFPOs and Cl-PFESAs were more labile to deposit in fish livers than perfluorooctanoic and perfluorooctane sulfonic acids, respectively. Both field investigations and model simulations indicated that HFPO-TA and Cl-PFESAs, as well as the hydrogen-substituted analogs of 6:2 Cl-PFESA (6:2 H-PFESA), were biomagnified along the aquatic food chain. The bioaccumulation model simulation revealed that the accumulation of these emerging PFASs in fish was mainly through dietary intake, whereas gill respiration and fecal excretion facilitated their elimination. Metabolic transformation might also contribute to their elimination relative to the legacy ones.