Noontime day-to-day variability of ionosonde and incoherent scatter radar (ISR) measurements of the E layer are analyzed for two time periods: 9--27 March 1999 and 4 October--4 November 2002. E layer variability is found to be between 5 and 7% at midlatitudes for these periods. Polar latitudes demonstrate variability ranging from ~7 to 50%, resulting primarily from a combination of photochemical and auroral processes. In order to understand the relative importance of the various sources that drive the variability in the E layer, a one-dimensional time-dependent photochemical model of the Earth's upper atmosphere is developed. The model is able to reproduce E layer electron density and variability for both time periods at a number of mid- and low-latitude stations. It is shown that E layer variability is dominated by variations in the incident solar flux for mid- and low-latitude stations, while auroral ionization processes are estimated to contribute roughly 30% of the total variability observed at polar stations. Changes in the solar declination over the time periods studied are responsible for a secondary source of E layer variability at midlatitudes and for a primary source at high latitudes. Day-to-day changes in neutral atmosphere species (including observed NO densities) contribute the least to overall E layer variations, except at low latitudes, where their contribution to variability is comparable to variability induced by changes in solar declination.