The occurrence, riverine inputs and sources of perfluoroalkyl substances (PFASs) in Taihu Lake, one of the largest lakes in China, were investigated by measuring PFASs including the isomers of perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA) and perfluorohexanesulfonate (PFHxS) in the Lake and its main flow-in rivers. It was found that PFHxS, instead of PFOS or PFOA, was predominant both in the Lake and rivers (45.9-351ng/L), reflecting increasing demand of PFHxS in recent years. The riverine flux of PFASs into the Lake was estimated to be 1255kg/year. The percentage of linear (n-) PFOS and the ratio of 3+5m-/1m-PFOS were combined to indicate indirect source due to biodegradation of PFOS-precursors. The percentage order of n-PFOS was: the Lake (48.7%)the rivers (8.99)>ECF (electrochemical fluorination) product (6.76). These suggested that degradation of PFOS-precursors made distinct contribution to PFOS load in the waters, particularly in the Lake. The Lake and river waters had a consistent proportion of n-PFHxS (89.0%), which was slightly lower than the ECF product (96.0%), indicating it was mainly due to the release from production and application of PFHxS as an active ingredient.