Per-and polyfluoroalkyl substances (PFAS) are surface-active contaminants, which are detected in groundwater globally, presenting serious health concerns. The vadose zone and surface water are recognized as primary sources of PFAS contamination. Previous studies have explored PFAS transport and retention mechanisms in the vadose zone, revealing that adsorption at interfaces and soil/sediment heterogeneity significantly influences PFAS retention. However, our understanding of how surface water− groundwater interactions along river corridors impact PFAS transport remains limited. To analyze PFAS transport during surface water− groundwater interactions, we performed saturated−unsaturated flow and reactive transport simulations in heterogeneous riparian sediments. Incorporating uncertainty quantification and sensitivity analysis, we identified key physical and geochemical sediment properties influencing PFAS transport. Our models considered aqueous-phase transport and adsorption both at the air−water interface (AWI) and the solid-phase surface. We tested different cases of heterogeneous sediments with varying volume proportions of higher permeability sediments, conducting 2000 simulations for each case, followed by global sensitivity and response surface analyses. Results indicate that sediment porosities, which are correlated to permeabilities, are crucial for PFAS transport in riparian sediments during river stage fluctuations. High-permeable sediment (e.g., sandy gravel, sand) is the preferential path for the PFAS transport, and low-permeable sediment (e.g., silt, clay) is where PFAS is retained. Additionally, the results show that adsorption at interfaces (AWI and solid phase) has a small impact on PFAS retention in riparian environments. This study offers insights into factors influencing PFAS transport in riparian sediments, potentially aiding the development of strategies to reduce the risk of PFAS contamination in groundwater from surface water.