Freshwater lenses and their freshwater–saltwater transition zones are affected by climate change. Both sea-level rise and groundwater recharge influence freshwater volume and transition zone thickness. This study used a semi-generic approach to investigate climate change effects on freshwater lenses: a hypothetical island cross-section was combined with real-world boundary conditions. Sea-level projections including tides and storm surges, annual mean sea-level rise data, and monthly recharge projections of several climate models of the German barrier island Norderney in the North Sea were used to evaluate changes in freshwater lens and transition zone size between 1971–2000 and 2071–2100. Firstly, impacts of sea-level and recharge boundary conditions were investigated on islands of different widths. Secondly, a multi-parameter study was conducted focussing on variations of several relevant hydrogeological parameters. Results showed that it is very likely but not certain that freshwater lens volume and depth will decrease and transition zone thickness increase as a consequence of climate change. Model predictions revealed a strong dependency on the employed climate models and to a lesser extent on the hydrogeological parameters, at least for the parameter ranges used in this study. Of all hydrogeological parameters tested, the largest effects were caused by the hydraulic conductivity and its anisotropy. Furthermore, the study showed that boundary conditions have larger impacts on smaller islands. These results illustrate the importance of using projections from climate models in a sufficiently high resolution. Furthermore, their uncertainties and changes in variability of boundary conditions should be considered in studies about climate change impacts on freshwater lenses.