This study is based on complete subsurface datasets from three fields in the onshore Nile Delta (West Dikirnis, West Al-Khilala and El-Tamad) producing oil, gas and oil and gas, respectively from the Messinian reservoirs. Rock-Eval pyrolysis results, biomarker investigations and correlation between oil and bitumen extracts from the Pliocene and Messinian mudstones suggest that the oil was generated from an Upper Cretaceous-Lower Tertiary terrigenous, clay-rich source rock (type III kerogen) and deposited under oxic conditions in a fluvio-deltaic environment. Oil migrated from its marginally-mature source through the deep-seated faults and trapped into the Messinian reservoirs. Furthermore, the gas is mainly thermogenic generated from a mature Jurassic source rock enriched in terrigenous humic materials (type III kerogen). The pre-MSC Qawasim facies were derived mainly from pre-existing Cretaceous-Eocene sedimentary strata, felsic and intermediate igneous rocks by the Eonile network system and deposited in the Nile Delta in a northward prograding system. The Qawasim facies reservoir quality is largely controlled by marine influence and increases with deltaic progradation from prodelta to delta front and delta plain. On the other hand, the MSC Abu Madi facies were mainly derived from the pre-existing Qawasim facies and infilled the Messinian incised valley during three major infill facies. The MSC facies reservoir quality decreases upward with increased marine influence and transition from the continental aggradational-prograditional fluvial to the marginal marine retrogradational estuarine facies. Therefore, the best reservoir facies are the pre-MSC Qawasim proximal deltaic and the MSC Abu Madi fluvial facies.