The expansion of alien invasive species is a worldwide threat that affects most ecosystems. Islands and freshwater ecosystems are among the most vulnerable to species invasion, resulting in reduced biodiversity. In this study, we aimed to explore the floristic composition of the aquatic vegetation in four lagoons in southeastern Cozumel and assess the occurrence and abundance of alien and potentially invasive plants. We found a total of 43 aquatic or underwater herbaceous species that are subject to periodic flooding. Cluster analyses grouped the lagoons into two groups according to their floristic composition. The results demonstrate that alien and potentially invasive plants were dominant in 3 of the 4 lagoons, representing from 7 to 43% of the species. Six of these species were notably abundant, especially in three lagoons. Further, 2 species are considered among the 100 worst invasive species worldwide, although their abundance in Mexico remains relatively reduced. Five alien and potentially invasive species are terrestrial and grow on the shore of the lagoons, while one is aquatic. Urgent control and management actions are necessary. These should include (a) early detection and surveillance to determine if the alien species found behave as invasives; (b) understanding the relevance of invasive species; (c) preventing and intercepting; and (d) control and management. Habitat restoration, adequate legislation, collaboration between stakeholders, and raising awareness of the dangers of releasing or cultivating invasive species in the wild are also necessary.