Morphological sills condition sedimentary, water and fauna exchanges between different domains. In particular, sills are crucial factors to consider during the Messinian Salinity Crisis (MSC) palaeogeographic evolution (5.97–5.33 Ma) of the NW Mediterranean area. Here we focus on the Ebro River and its up to now unexplained short Messinian onshore length (~100 km) compared to that of the Messinian Rhone River (~480 km) despite similar present-day drainage basins. Thanks to an extensive seismic and borehole dataset, we present a new interpretation of a complete 270 km long Messinian Ebro incised-valley system course underneath the present-day continental margin and bathyal basin and its related distal detrital deposits. These results favour a syn-MSC or pre-MSC opening of the (endorheic) Ebro Basin to the Mediterranean. We propose a mechanism of retrogressive erosional process, localized at structural knickpoints that shift seaward through time. This mechanism resulted in the development of the complete incised-valley system and the falling stage system tract (FSST) during the MSC sea level fall with negligible or even null retrogressive inland erosion beyond the Catalan Coastal Range. The shifting of erosion-deposition is controlled by the pre-Messinian stepwise morphology and segmentation in the Valencia, Menorca and Liguro-Provence Basins. By comparison, the Rhone system is simpler, characterized by the key role of a single knickpoint (at the shelf-break) and a steeper continental slope. Both cases highlight the relationship between kinematic, segmentation and their relative morphologies, base-level fall and erosional/depositional response particularly well expressed during the outstanding MSC associated with a huge relative sea-level drop that we measured down to -1100 m below present day sea-level.