Elevated concentrations of per- and polyfluoroalkyl substances (PFAS) in drinking-water supplies are a major concern for human health. It is therefore essential to understand factors that affect PFAS concentrations in surface water and groundwater and the transformation of perfluoroalkyl acid (PFAA) precursors that degrade into terminal compounds. Surface-water/groundwater exchange can occur along the flow path downgradient from PFAS point sources and biogeochemical conditions can change rapidly at these exchange boundaries. Here, we investigate the influence of surface-water/groundwater boundaries on PFAS transport and transformation. To do this, we conducted an extensive field-based analysis of PFAS concentrations in water and sediment from a flow-through lake fed by contaminated groundwater and its downgradient surface-water/groundwater boundary (defined as ≤100 cm below the lake bottom). PFAA precursors comprised 45 ± 4.6% of PFAS (PFAA precursors + 18 targeted PFAA) in the predominantly oxic lake impacted by a former fire-training area and historical wastewater discharges. In shallow porewater downgradient from the lake, this percentage decreased significantly to 25 ± 11%. PFAA precursor concentrations decreased by 85% between the lake and 84–100 cm below the lake bottom. PFAA concentrations increased significantly within the surface-water/groundwater boundary and in downgradient groundwater during the winter months despite lower stable concentrations in the lake water source. These results suggest that natural biogeochemical fluctuations associated with surface-water/groundwater boundaries may lead to PFAA precursor loss and seasonal variations in PFAA concentrations. Results of this work highlight the importance of dynamic biogeochemical conditions along the hydrological flow path from PFAS point sources to potentially affected drinking water supplies.