Aquatic habitats are crucial for maintaining biodiversity and offering necessary ecosystem services, but pollution particularly microbiological contaminants is becoming a bigger danger to these systems. In order to evaluate the impact of pollution on microbial communities, biodiversity, and ecosystem functioning, this study investigates the ecotoxicology of microbial pollutants in aquatic settings. The study uses a multidisciplinary methodology to examine how pollution affects aquatic microbial populations and how those communities interact with other biotic and abiotic elements. It does this by combining field surveys, lab studies, and ecological modelling. The findings reveal significant alterations in microbial community composition, diversity, and function in response to pollution stressors, such as chemical contaminants, nutrient enrichment, and emerging pathogens. These disturbances can lead to cascading effects on higher trophic levels, affecting overall ecosystem health and resilience. The study highlights the importance of understanding the ecotoxicological effects of microbial contaminants for effective environmental management and conservation strategies. By elucidating the complex interactions between pollutants and microbial communities, this research contributes to advancing ecotoxicology and informing policy decisions aimed at safeguarding aquatic ecosystems and human health.