Submarine channels serve as routes transporting sediments across hundreds of kilometers from continental margins to the deepest parts of a basin’s seafloor. Consequently, owing to the influential role of gravity in determining the flow direction, these channels typically follow the steepest sloping paths, making paleo-drainage systems essential in reconstructing basin dynamics over geological periods. This research aims to document the interrelationships between tectonic tilting, rapid deposition of salt, and delta sediment propagation on basin morphology and consequently on sedimentary transport orientation. Here, we examine how the interplay between these geological processes influenced the orientation of submarine channels in the Levant Basin, our case study, over ∼10 m.y. During the late Miocene, sediments originating from the Levant continental margin were transported to the deep parts of the Eastern Mediterranean Sea (i.e., the Herodotus Basin) via a tectonic valley active until the Messinian Salinity Crisis. Later, exceptionally fast burial by salt and subsequent truncation of this evaporitic layer produced a nearly horizontal seafloor that redirected the regional drainage toward the basin’s center, with no connection to the adjacent and much deeper Herodotus Basin. This drainage configuration did not last long since tilting of the basin northward toward the Cyprus subduction zone and northward propagation of the Nile delta have rapidly reshaped basin morphology, resulting in a rotation of major sedimentary routes in the area. From a broad perspective, this research not only exemplifies how rapid salt burial can reset a basin’s drainage system but also has implications for geodynamic and geomorphic processes in evaporite-bearing sedimentary basins within tectonically active areas.