The occurrence and distribution of eleven perfluoroalkyl substances (PFASs) and the isomers of perfluorooctanoate (PFOA), perfluorooctanesulfonate (PFOS) and perfluorooctane sulfonamide (PFOSA) were investigated in water dissolved phase, sediment and suspended particulate matter (SPM) in two typical watersheds in China: Liao River Basin and Taihu Lake. The total concentrations of the PFASs in the dissolved phase were 44.4-781 ng/L in Liao River with high contribution of perfluorobutane sulfonate (PFBS) (75.7%) and PFOA (9.86%). The ∑PFASs in the dissolved phase in Taihu Lake was 17.2-94.4 ng/L with PFOA (39.8%), perfluorohexanoate (PFHxA) (30.1%) and PFOS (16.8%) as the dominant PFASs. The log Koc values of the PFASs in both SPM and sediment increased with increasing the perfluorinated carbon chain length. In Liao River Basin, the long chain perfluorocarboxylates (C10-12) bound with SPM contributed >30% to the total amount in water, suggesting that SPM could not be ignored when the environmental load of long chain PFASs in water was assessed. For the isomers of PFOA, PFOS and PFOSA, the linear isomers always displayed higher partition coefficients on particulate phases than the branched ones. An established isomer-profiling technique was applied to assess the relative contributions of various industrial origins for PFOA. In Liao River, when SPM was included in the water samples, there were contributions of PFOA from electrochemical fluorination (ECF) (∼55%), linear telomer (∼41%) and isopropyl telomer (∼4%) sources. While, the results based on the dissolved phase alone indicated more contribution of ECF (∼70%) source and lower contribution from linear telomer (∼26%) source. The discrepancy suggests that omitting SPM from water samples might lead to misunderstanding on the industrial origins of PFOA. In Taihu Lake, the isomer profile of PFOA was influenced mainly by ECF (∼88%) and partially by linear-telomer (∼12%) sources.