Mass balances of ten individual perfluorinated alkyl acids (PFAAs) in two nested pristine catchments in Northern Sweden with different sizes and hydrological functions were assembled for 2011–2012. Concentrations of PFAAs in rain and snowmelt, as well as in streamwater at the outlet of the two watersheds were measured and used to calculate PFAA atmospheric inputs to and riverine outputs from the catchments. The results generally showed a great excess of PFAA inputs for both catchments over the whole study year. However, during the spring flood period, the inputs and outputs were within a factor of 2 for several PFAAs and the streamwater showed PFAA patterns resembling the patterns in rain (as opposed to snowmelt), suggesting that snowmelt water infiltrating the ground had displaced water from the previous summer. Comparison of PFAA mass balances between the two catchments further suggested that atmospheric inputs of short-chain (replacement) perfluoroalkyl carboxylic acids had increased in the years before sampling, while inputs of the legacy perfluorooctane sulfonic acid had decreased. Overall, the mass balances indicate that a considerable portion of the PFAAs deposited from the atmosphere are stored in soil and may be released to surface and marine water environments in the future.