Simulations with the global ionosphere plasmasphere model driven by whole atmosphere model winds show significant longitudinal and day-to-day variations in the ionospheric parameters. Under fixed solar and geomagnetic activity levels, the contributions of lower atmosphere tides to the longitudinal and day-to-day variability in the upper atmosphere are estimated. Larger relative variability is found in the nighttime than in the daytime, which is consistent with observations. The perturbations from the lower atmosphere contribute about half of the observed variability in the ionospheric F2 peak plasma density under moderate solar activity and geomagnetic quiet conditions. The daily variability of the equatorial vertical plasma drifts is primarily driven by the day-to-day amplitude changes of the migrating semidiurnal tide, while the wave-4 and wave-3 longitudinal variations during September are dominated by the nonmigrating diurnal eastward propagating tides with zonal wave numbers 3 and 2, respectively.