The present study investigates the sedimentological analysis and petrophysical properties of the Messinian Abu Madi reservoir (AMR), offshore Nile Delta Basin in order to determine how facies heterogeneities control reservoir quality. This approach was performed by integrating core data from Mina-1 well and BE-1 well and wireline logs from four wells (BN-1, BN-2, BE-3 and Mina-1). Based on core studies, seven clastic facies have been identified, of which five form sandstone reservoirs. These facies have accumulated within a deep incised canyon-fill during four successive fluvial sub-environments; braided fluvial channel, point bar, floodplain, and abandoned channel. These fluvial sediments were changed into tidally influenced fluvial/estuarine deposits with aggradational-retrogradational stacking patterns due to a transgressive event during the Messinian time. Based on the well log petrophysical evaluation, the Abu Madi reservoir has a total porosity of 0.20–0.26 v/v and effective porosity in the 0.18–0.25 v/v range. Shale volume ranges from 0.04 to 0.09 v/v, and water saturation ranges between 0.15 and 0.45 v/v. Four reservoir rock types were recognized and interpreted as a function of composition and therefore having different petrophysical characteristics. RRT1 and RRT2 show good petrophysical properties and good reservoir quality. The best reservoir quality occurs in massive sandstones (RRT3), which have porosities up to 26% and permeabilities up to 1440 mD. RRT4 has a poor reservoir quality with porosity of 5.4% and permeability of 0.6 mD. The reservoir porosity heterogeneities and reservoir quality have been strongly impacted by the original composition and primary depositional facies.