We investigate the Stern layer of charged silica–water interfaces by calculating the ion–surface interaction from molecular dynamics simulations. The McMillan–Mayer potentials of mean force between a charged oxygen site and a lithium or cesium cation have been calculated. Contact ion pairs (CIPs) are important for the adsorption and desorption of ions, especially for lithium. An activation energy appears, which can result in a large estimated relaxation time. In the case of lithium, time scales needed to bind or unbind ions to and from the surface are found to be very long (up to the order of seconds for some surfaces), which implies that molecular dynamics cannot always be fully equilibrated. This work provides a new image of the Stern layer: it is not a continuous layer but a set of Bjerrum pairs. As a matter of fact, quantitative (macroscopic) treatments of such systems with localized surface charges require a three-dimensional model, contrary to the more commonly used one- or two-dimensional theoretical treatments.