Abstract. A new three-dimensional, time-dependent theoretical model of the Earth's low and middle latitude ionosphere and plasmasphere has been developed, to take into account the effects of the zonal E×B plasma drift on the electron and ion number densities and temperatures, where E and B are the electric and geomagnetic fields, respectively. The model calculates the number densities of O⁺(⁴S), H⁺, NO⁺, O₂⁺, N₂⁺, O⁺(²D), O⁺(²P), O⁺(⁴P), and O⁺(²P*) ions, the electron density, the electron and ion temperatures using a combination of the Eulerian and Lagrangian approaches and an eccentric tilted dipole approximation for the geomagnetic field. The F2-layer peak density, NmF2, and peak altitude, hmF2, which were observed by 16 ionospheric sounders during the 12–13 April 1958 geomagnetically quiet time high solar activity period are compared with those from the model simulation. The reasonable agreement between the measured and modeled NmF2 and hmF2 requires the modified equatorial meridional E×B plasma drift given by the Scherliess and Fejer (1999) model and the modified NRLMSISE-00 atomic oxygen density. In agreement with the generally accepted assumption, the changes in NmF2 due to the zonal E×B plasma drift are found to be inessential by day, and the influence of the zonal E×B plasma drift on NmF2 and hmF2 is found to be negligible above about 25° and below about –26° geomagnetic latitude, by day and by night. Contrary to common belief, it is shown, for the first time, that the model, which does not take into account the zonal E×B plasma drift, underestimates night-time NmF2 up to the maximum factor of 2.3 at low geomagnetic latitudes, and this plasma transport in geomagnetic longitude is found to be important in the calculations of NmF2 and hmF2 by night from about –20° to about 20° geomagnetic latitude. The longitude dependence of the night-time low-latitude influence of the zonal E×B plasma drift on NmF2, which is found for the first time, is explained in terms of the longitudinal asymmetry in B (the eccentric magnetic dipole is displaced from the Earth's center and the Earth's eccentric tilted magnetic dipole moment is inclined with respect to the Earth's rotational axis) and the variations of the wind induced plasma drift and the meridional E×B plasma drift in geomagnetic longitude. The study of the influence of the zonal E×B plasma drift on the topside low-latitude electron density is presented for the first time.