Molecular dynamics simulations based on a reactive potential with charge transfer were used to model the sol-gel synthesis of nanoporous silica gels in an aqueous environment. Three distinct structural regimes ranging from compact clusters to percolated silica networks were seen to emerge, depending on the solvent-to-silica ratio. A clear correlation was observed between cluster radius of gyration and the location of a broad peak in the silicon radial distribution function. A measure of structural defects was introduced to characterize the three regimes, which also show different growth kinetics as revealed by the relation between the diffusion coefficient and the condensation rate. The stability of the polymerized gel structures was assessed by measuring the change in the fractal dimension during supercritical drying.