Most charophyte species are threatened across Europe. Understanding their current and future distribution is a challenge for their conservation. We looked for species distribution models (SDM) and for increasing or decreasing species occurrence under a future climate scenario in Switzerland. Firstly, we modeled the occurrence of charophyte species in 1402 Swiss localities using presence–absence data and environmental variables (waterbody size, mean July temperature, July precipitation, soil calcium carbonate content and proportions of land used by agriculture and forest cover in the catchment area and in the surroundings). We used generalized additive models (GAM) to analyze the data. Secondly, based on the models, we predicted the occurrence of the species in 21,092 localities listed in Switzerland. Thirdly, we applied a climate scenario to our models (2 °C mean July temperature increase and 15% reduction in July precipitation) and predicted species occurrence under these new conditions. Twelve charophyte species were modeled successfully. The major driver of species distribution was the waterbody size, followed by climate and land-use variables. We detected predicted impacts of climate changes on the species occurrence and identified the potential winners and losers. About half of the species are predicted to become losers; they colonize the littoral zone of lakes. Other charophytes are potential winners; the majority of them colonize small waterbodies.