Closed (endorheic) sedimentary basins are key recorders of the climatic, erosional, and tectonic history of their surrounding topography, playing an active role in its evolution by changing the local geomorphological base level. When these basins become exorheic, the accelerated incision along the new fluvial network can excavate excellent stratigraphic outcrops, but this often removes the uppermost infill, and essential information about the late basin history is lost. Here we propose estimating the opening age and past elevation of captured closed basins by combining the flexural isostatic compensation of the eroded volume with available constraints on sediment age. We use this method to constrain the post-tectonic evolution of the Cenozoic Ebro basin in northeast Iberia. The similar results obtained for 4 dated stratigraphic columns show the robustness of the model and date the basin opening as 12.0–7.5 Ma, with a maximum paleoelevation of the basin of 535–750 m. The isostatic rebound associated with basin erosion, as much as 630 m in the center of the basin, may explain the absence of a canyon excavated by the Ebro River during the Mediterranean sea-level fall associated with the Messinian salinity crisis.