A high-resolution quantitative nannoplankton biostratigraphy has been established in four wells based on a total of 1241 subsurface samples to understand and improve hydrocarbon exploration and recovery in the offshore Nile Delta. Ninety-two nannofossil species were used to delineate stages/ages boundaries of the Miocene-Pleistocene succession and to construct the age-depth model. Empirical, semi-quantitative (Graphic Correlation), and quantitative (Unitary Associations ‘UA’) methods retained comparable results, suggesting that the data quality is a master variable in the biostratigraphic resolution of the studied sequence. The UA method retained a sequence of 22 UAs, which exceeded the empirical zones (15; CNM6-CNPL9 = NN4-NN19). However, these UAs were merged into 14 zones (UAZ) to enable correlation among sections. Age-depth models and the nannofossil abundance were used to estimate the sedimentation rates and identify the system tracts within the depositional cycles. The variation in sedimentation rate was attributed to the interplay between the sea level and Nile flooding, which controlled the terrigenous influx. Furthermore, the nannofossil diversity was linked to the sequence stratigraphic framework, where seven 3rd order sequences were identified and correlated with the Global Tethyan sequences. Moreover, the extinction rate has increased after the Messinian and is attributed to the Pliocene-Pleistocene sea-level highstand and invasion of deeper water rich in nutrients from the upwelling zone.