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Mio-Pliocene marine sediments comprise a discontinuous succession of carbonates and mixed carbonate siliciclastics on the Neogene shelf, which coincides with the Judean foothills area. On the slope (present Mediterranean coastal plain) the succession forms a wedge up to 1500 m thick of mostly fine-grained siliciclastics. The facies and architecture of the succession were influenced both by sea-level fluctuation and by the geodynamic change from thermally subsiding passive margins of the Arabo-African plate to a complex pattern of vertical movements that were associated with the breakup of the plate along the Red Sea Rift and Dead Sea Transform and the convergence of the African-Arabian and Eurasian plates. The Miocene eustatic succession is highly interrupted by vertical uplift tectonics, while the Pliocene eustatic succession is well represented despite the limited subsidence rates.

During most of the Early and Middle Miocene the shelf was tectonically uplifted above sea level, except for a short period of flooding in early-Middle Miocene times (N8, N9), when sea-level rise outstripped the uplift trend and a carbonate platform formed. The combination of tectonic uplift and sea-level fall prior to Late Miocene times (about 11 m.y. ago) resulted in the incision of a deep Beer Sheva Canyon, about 280 m below the shelf plane. Late Miocene sandy marlstones of the Bet Eshel cycle filled the Beer Sheva Canyon and spilled over it. They display a shallowing-upward trend, resulting in progradational clinoform stacking of the highstand systems tract, and channelled debris flows of the forced-regression systems tract. The Messinian desiccation event left the shelf emerged while depositing evaporites on the slope and in the basin. The degree of erosion during the Messinian was relatively minor because of arid conditions and limited runoff.

The Pliocene shelf shows a very low subsidence rate and compared to the Miocene succession is less affected by vertical uplifts. The Pliocene deposits are divided into six sequences. Their relative onlap curve largely corresponds to the sequence stratigraphic scheme in Sicily and the Gulf of Mexico. The two lowermost sequences (I and II) are composed of two sandy units; the lower forms an incised valley fill of shoreface deposits in the Beer Sheva area, and offshore sand deposits in distal-shelf areas (Besor). Although largely eroded, sequences I and II display maximum coastal onlap of all Pliocene cycles in the Beer Sheva Canyon area. Sequence III consists of mixed carbonate-siliciclastic grainstones of shoreface/foreshore deposits in the proximal area, and lower shoreface deposits in more distal areas. Sequences IV and V may be considered as a single 3rd-order cycle, where IV represents regressive lowstand (shale and sand) deposits and V represents prograding highstand (sandy grainstone) deposits. Sequence VI consists of marginal-marine to coastal plain (marlstones and sands) deposits and is largely truncated by the Ahuzam Conglomerate, representing a major uplift phase of latest Pliocene to Early Pleistocene age and marking the permanent emergence of the shelf.