There are many studies about the occurrence of legacy perfluoroalkyl acids (PFAAs) in fresh water ecosystem, but related information about emerging per- and polyfluoroalkyl substances (PFASs) is limited. In this study, along with ten legacy PFAAs, twelve non-PFAAs, including precursors of perfluorooctane sulfonic acid (PFOS) and emerging PFASs in the water, sediment and organisms in Taihu Lake, China, were investigated. As one replacement product of PFOS, perfluorohexane sulfonic acid (PFHxS) (mean: 69.3 ng/L) was the predominant PFAA in the water samples. Perfluorooctanesulfonamide (PFOSA) (mean: 0.190 ng/L) and 6:2 fluorotelomer phosphate diester (6:2 diPAP) (0.034 ng/L) were detected in all the water samples. Other emerging PFASs, such as N-ethyl perfluorooctanesulfonamidoa-cetic acid (NEtFOSAA), bis(perfluorohexyl) phosphinic acid (6:6 PFPiA) were frequently detected in the sediment and/or organisms. The organic carbon normalized sediment-water distribution coefficients (K_OC) and bioaccumulation factors (BAFs) of the PFASs generally increased with their log K_OW values. However, PFOSA, NEtFOSAA, 6:2 diPAP and 6:6 PFPiA displayed lower log BAFs, and/or lower log K_OC than expected, which may be due to biotransformation potentials and/or large molecular size. PFOSA was not biomagnified in the food web. For other emerging PFASs, the low detection frequencies in the organisms hampered us to evaluate their biomagnification potentials. The lower percentage of most of the branched PFOS isomers while higher percentage of 1 m-PFOS in the organisms suggested that there was indirect source of PFOS in the organisms. Similar to PFOS and PFOA, linear PFHxS isomer was preferentially enriched in organisms relative to its branched isomers.