The Messinian sequence rocks in the Nile Delta present prolific hydrocarbon reservoirs and are, therefore, of great importance from the aspect of petroleum exploration and development strategies. Yet, little is known about their tectonic provenance and depositional setting. This study focuses on the geochemical signatures archived in the Messinian siliciclastic sediments to employ them as a powerful tool to elucidate the basin evolution during the Messinian salinity crisis (MSC). The pre-MSC Qawasim sediments are texturally and compositionally immature. They are enriched in lithic fragments, foraminiferal bioclasts, and rounded heavy minerals suggesting a significant contribution from the pre-existing Cretaceous-Eocene mixed carbonate-siliciclastic rocks bordering the Nile Delta. In contrast, the textural and mineralogical compositions as well as a range of geochemical proxies (e.g., chemical index of alteration and weathering CIA, CIW as well as index of chemical variability ICV and Zr/Sc ratio) are in favor of prolonged weathering and at least second-cycle origin of the MSC Abu Madi sediments. The mutually correspondent elemental ratios (e.g., Al2O3/TiO2, K2O/Na2O, Zr/Hf, Rb/Sr, Cr/Zr, and Cr/Th) and uniform weathering trends are indicatives for a similar provenance of the pre-MSC Qawasim and MSC Abu Madi sediments.