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Abstract Air–water interfacial adsorption represents a major source of retention for many per‐ and poly‐fluoroalkyl substances (PFAS). Therefore, transient hydrological fluxes that dynamically change the amount of air–water interfaces are expected to strongly influence PFAS retention in their source zones in the vadose zone. We employ mathematical modeling to study how seasonal groundwater table (GWT) fluctuations affect PFAS source‐zone leaching. The results suggest that, by periodically collapsing air–water interfaces, seasonal GWT fluctuations can lead to strong temporal variations in groundwater concentration and significantly enhance PFAS leaching in the vadose zone. The enhanced leaching is more pronounced for longer‐chain PFAS, coarser‐textured porous media, drier climates, and greater amplitudes of fluctuations. GWT fluctuations and lateral migration above the GWT introduce a downgradient persistent secondary source zone for longer‐chain PFAS. However, the enhanced leaching and the secondary source zone are greatly reduced when subsurface heterogeneity is present. In highly heterogeneous source zones, GWT fluctuations may even lead to overall slower leaching due to lateral flow (in the GWT fluctuation zone and above the GWT) moving PFAS into local regions with greater retention capacities. Model simplification analyses suggest that the enhanced source‐zone leaching due to GWT fluctuations may be approximated using a static but shallower GWT. Additionally, while vertical 1D models underestimate source‐zone leaching due to not representing lateral migration, they can be revised to account for lateral migration and provide lower‐ and upper‐bound estimates of PFAS source‐zone leaching under GWT fluctuations. Overall, our study suggests that representing GWT fluctuations is critical for quantifying source‐zone leaching of PFAS, especially the more interfacially active longer‐chain compounds.