This study presents the effects of fluorescent dissolved organic matters (FDOM) on perfluoroalkyl acids (PFAAs) in western Lake Chaohu and its inflow rivers. The surface water samples from the 27 sites in western Lake Chaohu and its inflow rivers were collected in March and September 2013. The contents of PFAAs and the FDOM in the water samples were measured by a high-performance liquid chromatograph - mass spectrometer (HPLC-MS) and by a fluorescence spectrophotometer, respectively. The temporal-spatial distributions of PFAAs and FDOM, as well as their interrelationships, were investigated. Eleven PFAA components were detected, and the mean concentration of total PFAAs (TPFAAs) in western Lake Chaohu and its inflow rivers were 12.93 ± 5.19 ng/L and 11.84 ± 9.50 ng/L, respectively. PFOA was the predominant contaminant in two regions (7.13 ± 3.07 ng/L and 4.30 ± 2.14 ng/L) followed by PFHxA (1.72 ± 0.80 ng/L and 1.42 ± 1.41 ng/L) and PFBA (1.44 ± 0.78 ng/L and 1.37 ± 0.78 ng/L). The mean concentration of total FDOM in western Lake Chaohu and its inflow rivers were 220.0 ± 40.30 μg quinine sulfate units (Q.S.)/L and 406.3 ± 213.1 μg Q.S./L, respectively. The significant, positive correlations were observed between the PFAAs and FDOMs in both the lake area and the inflow rivers. However, no significant correlation was observed between PFAAs and the dissolved organic carbon (DOC) in the lake area. This finding indicated that the residues and distributions of PFAAs were significantly dependent on the compositions of dissolved organic matters (DOM) and not on the total content of DOM. Display omitted •The mean concentration of total FDOM was higher in western Lake Chaohu than in its inflow rivers.•The mean concentration of total PFAAs in western Lake Chaohu and its inflow rivers were similar.•The PFAAs in the dry season were significantly higher than those in the rainy season.•The significant positive correlations between the PFAAs and FDOMs in two regions•Humic substances and protein-like substances might have opposite effects on PFAAs' distributions.