The Middle–Late Miocene subsurface successions from the Southeastern Mediterranean coast were studied based on the calcareous nannoplankton. The study was established on three boreholes selected from the offshore Nile Delta region, which are Port Fouad M-5, Baltim-1, and NDOB-1. The boreholes were chosen from different petroleum concessions within the North Delta basin. The standard nannoplankton biozonation of Mediterranean areas was used in this study. The studied rock successions cover the Sidi Salim and Qawasim formations, which are widely recognized targets for gas exploration. The study of the calcareous nannoplankton in the studied successions revealed eight biozones, and they are from base to top: Sphenolithus heteromorphus (NN5), Discoaster exilis (NN6), Discoaster kugleri (NN7), Catinaster coalitus (NN8), Discoaster hamatus (NN9), Discoaster calcaris (NN10), Discoaster quinqueramus (NN11), and Amaurolitus tricorniculatus (NN12). The Langhian/Serravalian, the Serravalian/Tortonian, and the Tortonian/Messinian boundaries were defined and discussed. The biochronological dates of the identified nannoplankton biozones were used to calculate the sedimentation rates of the studied rock successions. The calculations revealed two cycles of successive changes of sedimentation rates, which are attributed to regressions phases in Sidi Salim and Qawasim formations.