Recent improvements in the Soil and Water Assessment Tool (SWAT) model take account of hydrological processes controlling a variable source area (VSA). This model, SWAT-VSA, accounts for changes in the nature and extent of the VSA over the course of a hydrological cycle by considering global catchment storage capacity, which varies with soil moisture between threshold values whose spatial distribution is determined by topography. The objective of this work is to evaluate the contribution of several aquifers with specific storage capacities to global catchment storage, its dynamics; and subsequent effects on VSA and non-point-source pollution. For this purpose, a method called SWAT-mVSA (SWAT-multi VSA) was used in a catchment representative of the agricultural conditions of large perialpine lakes to calculate soluble reactive phosphorus (SRP) fluxes because SRP has a major influence on receiving waters. SWAT-mVSA predicted components of the hydrological balance and SRP fluxes more accurately than SWAT-VSA. This underlines the importance of VSAs in mobilizing and transporting non-point-source pollutants such as nutrients, pesticides, or bacteria.