Global changes are responsible for the movement of species. While many research emphasize the spread of alien or invasive alien species, the rapid spread of rare, native species is poorly study. In our studies, we focused on Trapa natans, a species that is considered a strictly protected plant species in Europe, but is considered an alien invasive species in North America and Australia. The aim of the study was to analyze the historical and current occurrence of T. natans at the northern range of this species (Poland, Central Europe) and, based on future climate projections (wordClim), to determine its potential spread in Europe by modeling the occupation area of available habitats in Europe. We found a rapid spread of T. natans in Poland associated with increasing temperatures. Statistical analyzes showed that the mean temperature of the warmest quarter and precipitation of the driest month are the most important climatic variables determining habitat suitability for T. natans. The model for 2021–2040 showed an expansion of habitats suitable for the species to the north (Great Britain and Ireland, Scandinavia), to the east (Germany and Central Europe), to the northeast (Eastern Europe, e.g., Lithuania, Latvia), and to the south (Italy and Southern Europe). In the next two time periods (2041–––2060 and 2061–––2080), the models showed that the entire European area is suitable for colonization by the species, with the exception of the high mountain regions and Spain. T. natans is a representative species whose distribution and recent range changes allow us to track aquatic species feedbacks to climate change in the species’ home range and is a good ecological indicator of global warming. The message for conservationists is that the status of species classified as rare needs to be urgently reviewed.