The impact of human activities on the environment's living organisms is increasing day by day. A prime example is the development of medicine and the pharmaceutical industry, which leads to various pharmaceuticals ending up in wastewater, including antibiotics, a widely used type. These ecotoxicological agents have been shown to cause many undesirable outcomes. In our study, we aimed to investigate the impact of one such widespread antibiotic, Trimethoprim (TMP), on the survival and microbiome composition of five different Hydra oligactis strains (C2/7, X11/14, M83/4, T3/2, T3/1). We tested six concentration groups (control, 0.1, 1, 10, 100, and 1000 µg/L). The results revealed that strains T3/1 and T3/2 were unaffected by antibiotics. However, strains C2/7 and M83/4 showed decreased survival at 1 µg/L. Conversly, strain X11/14 manifested increased survival at concentrations of 10 and 100 µg/L compared to the control group. While analysis of alpha and beta diversity did not reveal significant effects on hydra microbiomes, differential abundance analysis identified specific taxonomic groups affected by TMP. Overall, we observed high intraspecific variation, which is crucial for better understanding population dynamics in complex real environments.