Short-chain perfluoroalkyl acids (PFAAs), which have less than seven fluorinated carbons, have been introduced as substitutes for eight-carbon homologue products. In this study, water, sediment, and biological samples (fish and plant) were collected from Tangxun Lake, which is located near a production base of the fluorochemical industry in Wuhan, China. Perfluorobutane sulfonate (PFBS) and perfluorobutanoic acid (PFBA) were the predominant PFAAs in surface water, with average concentrations of 3660 ng/L and 4770 ng/L, respectively. However, perfluorooctane sulfonate (PFOS) was the most abundant PFAA in sediments, with an average concentration of 74.4 ng/g dw. The organic carbon normalized distribution coefficients (KOC) indicated that short-chain PFAAs (CF2 < 7) tended to have lower adsorption potentials than PFOS, perfluorooctanoic acid (PFOA), and longer perfluoroalkyl chain compounds. PFBS and PFBA could transport to a farther distance in the horizontal direction along the water flow and infiltrate into deeper depths in the vertical direction. However, levels of PFOS and PFOA in water dropped exponentially along the current, and their proportions were decreased gradually with the increasing depth in sediment cores. Furthermore, values of log bioconcentration factor (BCF) of the short-chain PFAAs were all relatively low (<1), indicating no bioaccumulation potentials for short-chain PFAAs in aquatic species.