Non-native aquatic plants are amongst the major threats to freshwater biodiversity and climate change is expected to facilitate their further spread and invasiveness. To date, in Croatia, no complete list of non-native extant and horizon aquatic plants has been compiled nor has a risk screening been performed. To address this knowledge gap, 10 extant and 14 horizon aquatic plant species were screened for their risk of invasiveness in the Pannonian and Mediterranean regions of Croatia under current and predicted (future) climate conditions. Overall, 90% and 60% of the extant species were classified as high risk for the Pannonian and Mediterranean regions, respectively, under both climate scenarios. Of the horizon species, 42% were classified as high risk under current conditions and, under climate change, this proportion increased to 78%. The ‘top invasive’ species (i.e. scored as very high risk) under both climate conditions and for both regions were extant Elodea nuttallii and horizon Lemna aequinoctialis. The horizon Hygrophila polysperma was very high risk for the Mediterranean Region under current climate conditions and for both regions under projected climate conditions. Azolla filiculoides, Elodea canadensis, Egeria densa and Utricularia gibba were also classified as high risk under current climate conditions and, after accounting for climate change, they became of very high risk in both regions. Further, Gymnocoronis spilanthoides and Lemna minuta were found to pose a very high risk under climate change only for the Pannonian Region. It is anticipated that the outcomes of this study will contribute to knowledge of the invasiveness of aquatic plants in different climatic regions and enable prioritisation measures for their control/eradication.