Based on seismic and well data, this study reports for the first time on the Messinian mixed siliciclastic-carbonate succession in the onshore Nile Delta, Egypt. It records a regressive-transgressive dominated siliciclastic succession followed by post-transgressive highstand carbonates accumulated prior to the Mediterranean forced regression phase of the Messinian salinity crisis (MSC). On seismic, the studied succession comprises two different seismic units. The lower corresponds to the prograding siliciclastic facies; whereas the upper unit represents the mounded carbonate build-up. The prograding siliciclastic succession encompasses the coarsening upward facies of basal prodelta followed by delta-front and delta-plain sediments. The cored interval constitutes the upper part of the prograding cycle consisting of floodplain mudstones, argillaceous interdistributary bay sandstones and coarse-grained distributary channel-fill sandstones. These are followed by a transgressive 3.5m thick interval of calcareous tidal sand bars deposited after the abandonment of the delta due to the pre-MSC transgressive phase. Post-transgressive highstand carbonate build-up is characterized by subtropical-temperate rhodalgal and foramol facies. The abundant rhodoliths assemblages dominated by melobesioids (> 90%) suggesting a shallow-water depositional conditions (~10–20 m). Pervasive dolomitization of carbonates suggests upward shallowing of the carbonate platform and a transition into evaporative supratidal sabkha conditions subsequent to the onset of the MSC. The carbonate platform was subaerially exposed, and meteoric water incursion led to formation of karst depressions (> 0.5 km wide) locally infilled by continental argillaceous sediments. Offshore transition wackestone/mudstone and mudstone deposits of the post-MSC marine flooding (Zanclean) effectively sealed the karstified carbonates forming excellent stratigraphic-type hydrocarbon traps. Besides the economic significance of the present results, this study provides a new onshore evidence of the Late Messinian sea-level drawdown and extends our knowledge of basin evolution of the Mediterranean realm around the MSC.