Climate change, worsening freshwater quality, and anthropogenic factors have caused water caltrop to lose approximately 80% of its habitat in Poland since the early 1980s. The presence of this plant species has substantially changed since the end of the 19th century. Our aim in this study was to examine the habitat and conservation status of Trapa natans in the Szumirad reservoir and Nowokuźnicki pond reserve in Poland and to indicate sources of potential hazards for the analyzed population. To achieve this aim, we spatially analyzed the changes in the total reservoir area, dynamics of species population, physico-chemical parameters of water, and climatic data. For the Szumirad reservoir, we observed substantial changes in water caltrop quantity and condition. For the Nowokuźnicki pond reserve, we found a serious threat to the Trapa habitat posed by the developing Nupharo–Nymphaeetum albae association, which is a strong competitor of nymphaeids. The obtained results indicated that surface waters localized in protected areas might play an important role in maintaining the population of water caltrop. On the basis of our analyses of selected populations, we emphasize that present protection procedures should be supplemented with the active protection of the species.