Using an in–house developed Quasi Two–Dimensional (QTD) physics–based ionospheric model, the impact of E × B drift velocity on the vertical distribution of the electron density over the equatorial latitude has been investigated. The vertical drift measurements from (a) drift analysis software of Digisonde (b) derived from Digisonde ionograms (c) calculated from the Scherliess–Fejer (SF) model, and (d) obtained from the magnetometer ΔH measurements have been used in this study. Four quiet days in a low solar activity year, representing four seasons of the year 2010, have been chosen for the study. The model–derived electron density profiles using the vertical drifts from all four methods matched well with the Digisonde observation below ∼150 km at all the Local Times (LTs) for all 4 days. However, since the Digisonde–derived drifts were very low, centered mostly around zero, it led to the overestimation/underestimation of the F–region peak plasma density (nmF2)/height (hmF2). The model simulated electron density profiles using the SF model, and ΔH derived vertical drifts showed good agreement with the observation up to an altitude of ∼350 km. The study showed that vertical drift is a factor that controls the nmF2 trough around noon over the equatorial latitude. It is seen that plasma diffusion occurs only beyond an altitude of 350 km, while the range of altitudes between 320 and 350 km acts as the “diffusion threshold height.” This finding has significant implications for understanding plasma dynamics in the equatorial ionosphere.