The Messinian Salinity Crisis (MSC) resulted from changes in the Atlantic-Mediterranean connectivity in the Alboran Basin, a region with a complex and debated geodynamic configuration. Since the MSC, this basin's topography and its record of the Messinian Erosional Surface have been subject to vertical motions due to sediment accumulation, tectonic deformation, isostasy, and latent effects of thermal cooling after extension and magmatic arc formation. The objective of this work is to restore these contributions to post-Messinian subsidence in order to quantify the original depth of formation of the MSC features. We do this by performing a pseudo-3D planform flexural isostatic reconstruction of the Messinian Erosion Surface mapped from an extensive set of seismic reflection data. We focus on identifying the most likely position of the gateway between Atlantic and Mediterranean, the effect of a drawdown on gateway topography and connectivity, and the depth of proposed erosional features related to the Messinian lowstand. The results indicate that the depth of the Alboran Basin by the end of the Messinian was about 500 m shallower than nowadays, but over 500 m deep on average, reaching depths of >1000 m in most subbasins, even when accounting for the possible ∼300 m isostatic rebound caused by water unloading in a largely desiccated Alboran Sea during the MSC. Although these results are compatible with volcanic cones locally emerging above sea level at the East Alboran Volcanic Arc during the Messinian, several lows remaining in the reconstruction suggest that that region is unlikely to have been the sill between Atlantic and Mediterranean at that time, unless the basin saw unconstrained dynamic topography contributions of over −500 m. Full desiccation of the Alboran Basin implies an uplift of up to 100 m at the Strait of Gibraltar, and uplift rates too high to be counteracted by erosion, suggesting that full disconnection and the main corresponding evaporative drawdown took place only once. The terraces and canyons in the West Alboran are restored to depths between 250 and 550 m (shallowest terrace) and 750–1500 m (deepest terrace), and cannot be clearly linked to a single, stable water level during the MSC, pointing to climate-controlled variations in the water level during the isolation phase.