Following the termination of the Messinian salinity crisis ~5.3 million years ago, massive sedimentation in the Eastern Mediterranean Sea formed the huge Nile Delta. Alongside delta propagation, a continental shelf was accreted along the Levant margin. For several decades it was assumed that these two sedimentary structures were closely connected. Levant shelf deposits are composed of Nile-derived sediments and present-day measurements show that sand is currently being transported alongshore from the Nile Delta to offshore Israel. This study reexamines the existing paradigm about sediment transport and shelf-delta connection. We show that longshore sand transport is just a small part of a much larger process termed here margin-parallel sediment transport (MPST). Sand is transported in a nearshore shallow-water belt where marine currents are highly energetic. At the same time, shale is transported at greater depths over the deeper shelf and the continental slope where marine currents are weaker. To model the accretion of the Levant shelf alongside the Nile Delta we use a 3D, diffusion-based, stratigraphic modeling tool (DionisosFlow) with a new module representing MPST. Our results show that margin-parallel transport of silt and clay in the deeper waters accounts for the bulk of deposition offshore Israel and is responsible for the development of the Levant shelf. Moreover, though MPST has begun coevally with delta formation, massive accretion of the Levant shelf was delayed by 2–3 My. Initially, a continental shelf formed offshore Sinai, then offshore Israel, and most recently along the Lebanon coast. Our model also demonstrates the significant lithological differences observed between sedimentation in front of the Nile River mouth and along adjacent continental margin. High energy down-slope sediment transport carries sand, silt, and clay, whereas margin-parallel currents are relatively weak and carry mainly silt and clay. One exception within the margin-parallel system is the highly energetic nearshore current that transports sand. Thus, we point out, MPST is an efficient separator between shale and sand.