The evolution of permafrost in cold regions is inextricably connected to hydrogeologic processes, climate, and ecosystems. Permafrost thawing has been linked to changes in wetland and lake areas, alteration of the groundwater contribution to streamflow, carbon release, and increased fire frequency. But detailed knowledge about the dynamic state of permafrost in relation to surface and groundwater systems remains an enigma. Here, we present the results of a pioneering ∼1,800 line-kilometer airborne electromagnetic survey that shows sediments deposited over the past ∼4 million years and the configuration of permafrost to depths of ∼100 meters in the Yukon Flats area near Fort Yukon, Alaska. The Yukon Flats is near the boundary between continuous permafrost to the north and discontinuous permafrost to the south, making it an important location for examining permafrost dynamics. Our results not only provide a detailed snapshot of the present-day configuration of permafrost, but they also expose previously unseen details about potential surface – groundwater connections and the thermal legacy of surface water features that has been recorded in the permafrost over the past ∼1,000 years. This work will be a critical baseline for future permafrost studies aimed at exploring the connections between hydrogeologic, climatic, and ecological processes, and has significant implications for the stewardship of Arctic environments.