In this paper the evolution of the groundwater chemical composition in aquifers from large sedimentary basins over geological timescale is investigated. The solutes upon which we focus are sulfate, chloride, and sodium because they often display concentration gradients at the regional scale and they are largely undersaturated with respect to any mineral. To explain these gradients, several phenomena are studied: leakage, dissolution of minerals or ion exchange within an aquifer, and dissolution of minerals or ion exchange from an overlying aquitard. Assuming local equilibrium, the study of dissolution within the aquifer shows that the minerals containing sulfate and chloride must have been leached out rapidly after aquifer flushing and should not exist after one million years of water flow. In addition, a simplified model of leakage shows that dissolution of minerals embedded in an aquitard could deliver a flux of ions able to explain significant gradients within the aquifer. Without water transfer from aquitard to aquifer, diffusion from the aquitard can also lead to significant concentration gradient along the aquifer. A detailed study of ion exchange shows that the clays existing in the aquifer are rapidly (thousands of years) saturated with calcium and will not release sodium later. On the other hand, exchange from the aquitard clays, followed by diffusion, is able to change sodium and calcium concentrations significantly over geological time intervals in the aquifer. The intensities of each process studied are compared. It is shown that given the assumptions made, the influence of each process can be differentiated where the aquifer-aquitard system is well enough characterized. Analysis of aquifers with clay beds, detailed in the discussion, suggests that these layers may play a secondary role over geological timescales. However, they can lead to disconnected parts of the aquifer that can show different water chemistry. Our work suggests that the composition of major aquitards may have a significant effect on the chemistry of the aquifer water.