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Abstract 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.