Perfluoroalkyl acids (PFAAs) are highly persistent chemicals that are ubiquitously found in the environment. The atmospheric degradation of precursor compounds has been identified as a source of PFAAs and might be an important pathway for contamination. Lake Vättern is one of Sweden's largest lakes and is an important source for drinking water. In addition to contamination via atmospheric deposition, the lake is subject to several potential contamination sources via surface water inflow. The relevance of different sources is not well understood. A mass balance of selected PFAAs was assembled based on measured concentrations in atmospheric deposition, surface water from streams that constitute the main inflow and outflow, and surface water in the lake. The largest input was seen for trifluoroacetic acid (150 kg/year), perfluoropropanoic acid (1.6 kg/year), perfluorobutanoic acid (4.0 kg/year), and perfluoro-octanoic acid (1.5 kg/year). Both atmospheric deposition and surface water inflow was found to be important input pathways. There was a positive correlation between the input of most perfluoroalkyl carboxylic acids via atmospheric deposition and global radiation and between the input via surface water inflow and catchment area. These findings highlight the importance of atmospheric oxidation of volatile precursor compounds for contamination in surface waters.