This letter presents a study of equatorial F region irregularities using the NRL SAMI3/ESF model, comparing results using a two-dimensional (2-D) and a three-dimensional (3-D) electrostatic potential solution. For the 3-D potential solution, two cases are considered for parallel plasma transport: (1) transport based on the parallel ambipolar field, and (2) transport based on the parallel electric field. The results show that the growth rate of the generalized Rayleigh–Taylor instability is not affected by the choice of the potential solution. However, differences are observed in the structures of the irregularities between the 2-D and 3-D solutions. Additionally, the plasma velocity along the geomagnetic field computed using the full 3-D solution shows complex structures that are not captured by the simplified model. This points out that only the full 3-D model is able to fully capture the complex physics of the equatorial F region.