Microbes from the surrounding environment serve as potential colonizers for animal microbiome. We studied the impact of environmental water on microbial communities in freshwater Hydra using correlational and experimental methods. Hydra polyps and water samples were collected from 15 Hungarian lakes, and bacterial community composition was assessed via 16S sequencing. Correlation analyses and neutral modeling evaluated the impact of water microbiota on geographical variation in Hydra microbiota. In the lab, field-collected Hydra polyps from three populations were cultured in either native water or water from another location. Our findings revealed that lake water bacteria significantly contribute to Hydra microbial communities, but the compositional profile remained stable when cultured in different water sources. These results indicate that while water serves as a source for bacterial colonization, Hydra's microbial communities demonstrate resilience to environmental invasion from freshwater sources.