The infamous “master manipulators” – intracellular bacteria from the genus Wolbachia – infect a broad range of phylogenetically diverse hosts in terrestrial ecosystems. Wolbachia have important impacts on the ecology and evolution of their hosts with documented effects including induced parthenogenesis, male killing, feminization, and cytoplasmic incompatibility. On the other hand, data on Wolbachia infection in non-terrestrial invertebrates is scarce. Sampling bias and methodological limitations are among the reasons we are unable to detect these bacteria in aquatic organisms. Here we presented a metabarcoding method to detect the co-occurrence of different Wolbachia strains in new, to science, host species: water bears (Tardigrada), freshwater arthropods, and mollusks. In addition, we describe a new Wolbachia strain (supergroup V) and identify a very widespread supergroup A. This supergroup could indicate transinfection and Wolbachia abilities to switch hosts within new environmental conditions, and between hosts that are ecologically connected. Future research should focus on ecological and evolutionary relationships between a new host species and the “master manipulator”.