In coastal-zone fields with a high groundwater level and sufficient rainfall, freshwater lenses are formed on top of saline or brackish groundwater. The fresh and the saline water meet at shallow depth, where a transition zone is found. This study investigates the mixing zone that is characterized by this salinity change, as well as by cation exchange processes, and which is forced by seepage and by rainfall which varies as a function of time. The processes are first investigated for a one-dimensional (1D) stream tube perpendicular to the interface concerning salt and major cation composition changes. The complex sequence of changes is explained with basic cation exchange theory. It is also possible to show that the sequence of changes is maintained when a two-dimensional field is considered where the upward saline seepage flows to drains. This illustrates that for cation exchange, the horizontal component (dominant for flow of water) has a small impact on the chemical changes in the vertical direction. The flow’s horizontal orientation, parallel to the interface, leads to changes in concentration that are insignificant compared with those that are found perpendicular to the interface, and are accounted for in the 1D flow tube. Near the drains, differences with the 1D considerations are visible, especially in the longer term, exceeding 100 years. The simulations are compared with field data from the Netherlands which reveal similar patterns.