Abstract Prior to injecting CO 2 at the Ketzin pilot site for carbon storage near Berlin, Germany, several pumping tests were conducted in the three wells drilled for CO 2 injection and monitoring. To characterize subsurface properties and help interpret the behavior of CO 2 injected in the subsequent experiments, we calibrate a groundwater flow model for numerically simulating the pumping tests. The model honors the vertical layering of the storage formation: a sandstone layer of 6–18 m thickness embedded in a thick low-permeability mudstone (about 70–80 m). Model calibration involves estimating the spatial distribution of permeability in 13 zones for the sandstone layer while keeping the permeability of the mudstone at a fixed low value (1 × 10 −15 m 2 ). The calibrated model produces system responses that are in good agreement with the measured pressure drawdown data, suggesting that the essential flow processes occurring during the pumping tests are well captured. The estimated permeability distribution indicates that heterogeneity is significant and that the pilot site acts as a semi-closed hydrogeologic system with one side effectively blocked by a low-permeability region. Of the three wells analyzed (Ktzi 200, Ktzi 201, and Ktzi 202), the inversion algorithm finds permeable zones connecting Ktzi 202 with Ktzi 200/Ktzi 201, while a low-permeability zone is found between Ktzi 201 and Ktzi 200. The calibrated results are consistent with the core logging and crosshole baseline ERT data and can help explain the migration of the CO 2 plume, inferred from 3-D seismic surveys and ERT data obtained during the subsequent CO 2 injection experiment. A proof-of-concept model shows that the presence of a low permeability zone between Ktzi 200 and Ktzi 201 is in fact consistent with the monitored CO 2 arrival times at both wells if this zone of low effective permeability contains a thin high-permeability layer allowing for fast transport. Presence of a thin layer of high-permeability sandstone within a thick low-permeability layer does not significantly affect the pressure response in a pumping test as the effective permeability is still low, but it has a much larger impact on the CO 2 arrival time by providing a preferential path for the CO 2 migration.