Emerging groundwater contaminants such as per- and polyfluoroalkyl substances (PFAS) may impact surface-water quality and groundwater-dependent ecosystems of gaining streams. Although complex near-surface hydrogeology of stream corridors challenges sampling efforts, recent advances in heat tracing of discharge zones enable efficient and informed data collection. For this study we used a combination of streambed temperature push-probe and thermal infrared methods to guide a discharge-zone-oriented sample collection along approximately 6 km of a coastal trout stream on Cape Cod, MA where groundwater discharge constitutes approximately 95% of total streamflow. Eight surface-water locations and discharging groundwater from 24 streambed and bank seepages were analyzed for dissolved oxygen, specific conductance, stable water isotopes, and a range of PFAS compounds which are contaminants of emerging concern in aquatic environments. The results indicate a complex system of groundwater discharge source flowpaths, where the sum of concentrations of six PFAS compounds (Environmental Protection Agency third Unregulated Contaminant Monitoring Rule UCMR 3) showed a median concentration of 52 331 (SD) ng/L with two higher outliers and three discharges with non-detection of PFAS. Higher UCMR 3 PFAS concentration was related -0.66 (Spearman Rank, p<0.001) to discharging groundwater that showed an evaporative signature (deuterium excess), indicating flow through at least one upgradient kettle lake. Therefore, more regional groundwater flowpaths originating from outside the local river corridor tended to show higher PFAS concentrations as evaluated at their respective discharge zones. Conversely, UCMR 3 PFAS concentrations were typically low at discharges that did not indicate evaporation and were adjacent to steep hillslopes and, therefore, were classified as locally recharged groundwater. Previous research at this stream found that the native brook trout favor discharge points of groundwater recharged on local hillslopes for spawning, likely in response to generally higher levels of dissolved oxygen compared to discharge zones located further away from hillslopes. Our study shows that the trout may thereby be avoiding emerging contaminants such as PFAS in groundwater recharged farther from the stream.