The spatial distribution of 10 perfluoroalkyl acids including linear and branched (six monotrifluoromethyl isomers) perfluorooctane sulfonate (PFOS) in surface water was investigated in Huai River Basin and Taihu Lake in Jiangsu Province, China. In the water samples from Huai River Basin, perfluorooctanoic acid (PFOA) and PFOS were the predominant compounds (mean 18 ng/L and 4.7 ng/L, respectively), while in samples from Taihu Lake, PFOA, perfluorohexanoic acid (PFHxA), and PFOS were the predominant compounds (mean 56 ng/L, 19 ng/L, and 15 ng/L, respectively). Branched PFOS (Br-PFOS) isomers accounting for 48.1% to 62.5% of total PFOS were enriched in all samples from Taihu Lake, compared to technical electrochemical fluorination (ECF) PFOS (Br-PFOS ∼30.0%), while the similar phenomena were not found in samples from Huai River Basin (Br-PFOS 29.0-35.0%). Principal component analysis (PCA) on the percentages of the individual isomer showed that the first two components accounted for 78.4% and 15.3% of the overall observed data variance. Samples from Huai River Basin were grouped together with the ECF PFOS standard suggesting the profiles were similar, while samples from Taihu Lake were grouped by themselves, suggesting that isomer profiles in these samples were different from that of Huai River Basin. The obvious difference in isomer profiles probably results from the different environmental behaviors of PFOS isomers and/or unknown sources (PFOS or PFOS precursors).