After global commercialization of short-chain perfluoroalkyl acids (PFAAs) as substitutes to conventional long-chain PFAAs by the major manufacturers, two fluorine industry parks for production of short-chain PFAAs located in the Daling River Basin of northern China have developed rapidly in the last few years. This study provides a systematic assessment of sources, emissions, transportation, and potential risks of the PFAAs in this area. The C4 perfluorobutane sulfonic acid (PFBS) and perfluorobutanoic acid (PFBA) were the predominant short-chain PFAAs in river water, with maximum concentrations of 2.90 and 1.35 μg/L, respectively. Park 1 equipped with a telomerization process was identified to be the source of linear and branched mixtures of PFBS, PFBA, and perfluorooctanoic acid (PFOA), while park 2 with an electrochemical fluorination process (ECF) was identified to be the source of linear and branched mixtures of PFBS and PFOA. Partition coefficients between water and sediment were consistent for C4-C8 perfluoroalkyl carboxylic acids (PFCAs) but directly proportional to C9-C11 PFCAs and perfluoroalkyl sulfonic acids (PFSAs). Analysis on the health risk of PFBS and PFBA suggested that they were not without risk since short chain PFAAs are known to be recalcitrant during water treatment.