It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two orders of magnitude. The decrease in water exchange frequency with progressive embedding of surface calcium ions is thought to be rate limiting to subsequent attachment of carbonate ions during calcite growth. Therefore, a process-based calcite growth kinetics model, reparameterized using the water exchange frequencies computed from molecular dynamics simulations, is used to illustrate the impact of these variations on kink-formation rate, step velocities and bulk growth rate. The calculated frequencies of kink formation show a strong variation with surface structures, which can be amplified depending on the saturation state and calcium to carbonate ratio of the solution. Modelled and measured step velocities and bulk growth rates are generally in agreement, showing that variations in calcite growth rates and step velocities observed experimentally might be at least partially induced by surface topography.