Seasonally warm summers in the Arctic produce supra-permafrost aquifers within the active layer. However, the magnitude of groundwater flow, the amount of dissolved carbon and nutrients, and the solute flow paths are largely unknown, but critical to quantifying downgradient contributions to surface waters (lakes and rivers). To develop approachable methods to quantify groundwater inputs in continuous permafrost watersheds, we selected Imnavait Creek watershed on the North Slope of Alaska as a representative headwater drainage. We conducted 1000 groundwater flow simulations based on topography of the watershed and varying aquifer hydraulic conductivity and saturated thickness values. We fitted a lognormal distribution to the resulting 1000 model outputs, and we derived n=1e6 possible discharge values based on Monte Carlo random sampling on the model outputs. The groundwater discharge values integrated across the watershed generally agree with observed streamflow in Imnavait Creek over 2 months. When groundwater discharge estimates were combined with in-situ measurements of groundwater-dissolved organic carbon and nitrogen concentrations, we found that Imnavait Creek’s organic matter load is also dominantly sourced from groundwater. Thus, riverine and lacustrine ecological and biogeochemical processes relate strongly to groundwater phenomena in these continuous permafrost settings. As the Arctic warms and the active layer deepens, it will become more important to understand and predict supra-permafrost aquifer dynamics.