Alien aquatic plants rank amongst the major threats to aquatic biodiversity and, since ongoing climate change is expected to facilitate their further spread, there is an urgent need for sound knowledge of their distribution and ecology. We collected published and unpublished data spanning the last ~130 years and performed the first comprehensive assessment of alien aquatic vascular plants in Slovakia with the following aims: (i) to prepare a national inventory, (ii) to assess the effects of climate and landscape on species diversity and (iii) to evaluate the habitat preferences of the species. The historical overview showed a strongly increasing trend in the number of alien species related to an increased amount of intensive research of aquatic vegetation over the last 30 years. Altogether, 20 neophyte alien aquatic plant taxa were recorded from 479 sampling sites. However, the species inventory seems to be far from complete and approximately 14 species are expected to remain undetected. Elodeacanadensis and E.nuttallii are the most frequently occurring alien aquatic plants, while eight other species have been found at a single site only. The majority of alien plants were deliberately introduced as aquarium ornamentals or released through pond waste. The fragmented information on local habitat conditions did not allow us to draw firm conclusions about the habitat preferences of alien aquatic plants. However, artificial water bodies are more frequently colonised by alien species than natural habitats (95% of aliens were found in artificial water bodies and 60% of them were recorded exclusively in these habitats) and many species have broad environmental tolerances (ability to colonise both standing and running waters, tolerances to a wide range of temperatures and water chemistry). Our results reaffirm the major role of increased temperatures and landscape modification in the distribution of alien aquatic plants and we can expect enhanced invasiveness and spreading of alien species into new habitats driven by climate change and land use intensification. Filling a main gap in the recognition of alien aquatic plant environmental preferences is a challenge for future research with the ultimate goal of maintaining natural aquatic plant diversity and ecosystem functioning.