Elodea nuttallii is an invasive plant widely distributed in many European freshwater habitats. The species has been recently added to the list of invasive alien species of Union concern (European Union (EU) Regulation 1143/2014). We aim to investigate the species’ potential distribution across the EU to provide a scientific basis for preventing further spread. To this end, we generated a model-based habitat suitability map for E. nuttallii in the EU, showing areas where the plant is most likely to establish and persist over time. The MaxEnt algorithm was used for implementing the map, taking into account environmental information and the most updated geographically referenced data on the species’ occurrence. The R package ENMeval and extraction of occurrence data at two spatial scales were used to compensate for sampling bias and model overfitting. Our results suggest that most of the EU suitable areas for the establishment of E. nuttallii are already occupied by the species. Still, there are many non-infested areas across the EU, and considering the rapid spread of E. nuttallii and the highly connected waterbodies in Europe, it is likely that these areas will be invaded in the near future. Among these, several areas fall within sites of the Natura 2000 protected network. We suggest that these areas should receive conservation priority, and early warning and rapid response mechanisms should be locally developed against new introductions of the species.