General biotic and abiotic contamination of water bodies is widely recognised. Zebra mussel (ZM) is commonly used in biomonitoring of water quality for its capacity to filter a great volume of water, and accumulate contaminants present in aquatic environments. The ZM’s digestive gland is a key organ in assessing the health status of the organism and concentrates high amounts of naturally occurring mixtures and pollutants. ZMs’ organs can adequately present the aquatic environment's health status and “early warning” for biomonitoring. The gut microbiota may significantly influence health and responses to environmental stressors of the organisms. The interaction between sentinel species and their microbiota has prompted questions, especially regarding their potential as indicators in environmental monitoring. Nevertheless, environmental factors can impact the composition and metabolism of gut microbiota responsible for breaking down and detoxifying xenobiotics. To advance our understanding of microbiota's role, we conducted both field and controlled studies. The first aim assesses the gut microbiota composition (16s rDNA sequencing) and physiological state in ZMs in-situ. The organisms were caged for 21 days in oligotrophic to eutrophic sites varying in food sources, bacterial load and water chemistry. In parallel, controlled experiments aimed to determine the optimal conditions (food quantity) for maximizing the filtration rate and effective removal of microorganisms. It occurred with the initial algae concentration of 10^5cells/mL and microbial populations at 10^5UFC/mL. Higher filtration rates cause higher contact with contaminants and feeding. This first step will enable us to investigate the impact of stressors under laboratory conditions on gut microbiota.