Patterns of species rarity have long fascinated ecologists, yet most of what we know about the natural world stems from studies of common species. A large proportion of freshwater plant species has small range sizes and are therefore considered rare. However, little is known about the mechanisms and geographical distribution of rarity in the aquatic realm and to what extent diversity of rare species in freshwater plants follows their terrestrial counterparts. Here, we present the first in–depth analysis of geographical patterns, potential deterministic ecogeographical factors and projected scenarios of freshwater vascular plant rarity using 50 × 50 km grid cells across Europe (41°N–71°N) and North America (25°N–78°N). Our results suggest that diversity of rare species shows different patterns in relation to latitude on the two continents, and that hotspots of rarity concentrate in a relatively small proportion of the European and North American land surface, especially in mountainous as well as in climatically rare and stable areas. Interestingly, we found no differences among alternative rarity definitions and measures when delineating areas with notably high diversity of rare species. Our findings also indicate that few variables, namely a combination of current climate, Late Quaternary climate–change velocity and human footprint, are able to accurately predict the location of continental centers of rare species diversity. However, these relationships are not geographically homogeneous, and the underlying factors likely act synergistically. Perhaps more importantly, we provide empirical evidence that current centers of rare species diversity are characterized by higher anthropogenic impacts and might shrink disproportionately within this century as the climate changes. Our reported distributional patterns of species rarity align with the known trends in species richness of other freshwater organisms and may help conservation planners make informed decisions mitigating the effects of climate change and other anthropogenic impacts on biodiversity.