Sparker (3000 J and 8000 J) and multichannel seismic reflection profiles across the Valencia trough show a Messinian unconformity incised by numerous valleys. The main feature of this surface is a large valley that generally underlies the present Valencia valley and is deeply entrenched into the Miocene deposits. The size of this palaeo-valley ranges from 0.5 km wide and 15–100 m deep at its western end, to 1.6–2.8 km wide and 200–250 m deep downstream. An important tributary system is observed, with a main canyon (6–8 km wide and 150–200 m deep) draining the Ebro margin, as well as many other smaller valleys draining the Catalan and Balearic margins. Downstream, other tributaries underlie the present canyons of the Catalan margin. The location of the tributary system is controlled by the Early Miocene rift structures. The relief of the Messinian surface is affected by post-Miocene deformation that results from salt diapirism, extensional faulting and related volcanism. Late Neogene to Quaternary volcanic edifices cut the Messinian surface and coincide with large residual magnetic anomalies. Lower Pliocene to Quaternary salt diapirism in the abyssal plain north of Menorca has created a series of structural highs. Between these highs are deep interdiapiric troughs or basins that have become sediment depocentres during the Plio-Quaternary. The complex network of erosional valleys from the Valencia trough continental margin demonstrates that the valley system in the basin was not related to the refilling of the Mediterranean, but to the Iberian and Balearic margin palaeodrainage that developed during the Messinian desiccation. The presence of at least three erosional unconformities suggests that there were alternating periods of flooding and retreat of Atlantic water during Messinian time. The Messinian subaerial margin with erosional valleys contrasts sharply with the Pliocene-Quaternary marine margin with progradational turbidite systems.