The external drivers and internal controls of groundwater flow in the thawed “active layer” above permafrost are poorly constrained because they are dynamic and spatially variable. Understanding these controls is critical because groundwater can supply solutes such as dissolved organic matter to surface water bodies. We calculated steady‐state three‐dimensional suprapermafrost groundwater flow through the active layer using measurements of aquifer geometry, saturated thickness, and hydraulic properties collected from two major landscape types over time within a first‐order Arctic watershed. The depth position and thickness of the saturated zone is the dominant control of groundwater flow variability between sites and during different times of year. The effect of water table depth on groundwater flow dwarfs the effect of thaw depth. In landscapes with low land‐surface slopes (2–4%), a combination of higher water tables and thicker, permeable peat deposits cause relatively constant groundwater flows between the early and late thawed seasons. Landscapes with larger land‐surface slopes (4–10%) have both deeper water tables and thinner peat deposits; here the commonly observed permeability decrease with depth is more pronounced than in flatter areas, and groundwater flows decrease significantly between early and late summer as the water table drops. Groundwater flows are also affected by microtopographic features that retain groundwater that could otherwise be released as the active layer deepens. The dominant sources of groundwater, and thus dissolved organic matter, are likely wet, flatter regions with thick organic layers. This finding informs fluid flow and solute transport dynamics for the present and future Arctic. Groundwater flow in permafrost watersheds is potentially a key component of global carbon budgets because permafrost soil stores vast amounts of carbon that could be mobilized due to a warming climate and the corresponding increase in soil thaw. In addition to carrying carbon, groundwater can supply important nutrients and solutes to surface waters. However, we do not yet understand the factors that control groundwater flow in soils above permafrost because saturation changes rapidly and continuously, and soil hydraulic properties are largely unknown. We created measurement‐informed calculations of groundwater flow from areas of permafrost with different characteristics and found that soil types, which vary based on the slope of the land surface, are the most important control. Near‐surface soils were identical in hillslopes and valleys, whereas deeper soils in hillslopes allowed for less groundwater flow than in valleys. In early summer, when only the near‐surface soils were thawed, groundwater flows in the hillslopes and valley were similar. In late summer, when the deeper soil was thawed, groundwater flow in the valley remained high, but flow in the hillslope was negligible. Our observations also showed that small mounds on the land surface caused groundwater to be trapped behind underground ice dams. Detailed measurements of hydraulic head, hydraulic conductivity, and saturated thicknesses in active layers were made over time and spaceThree main soil layers consistently comprise the stratigraphy of the active layer across the studied Arctic watershedGroundwater flow depends most on the depth of the water table and the subsurface stratigraphy, which varies based on landscape type