Aquaculture effluent treatment is a critical aspect of sustainable aquaculture practices, ensuring environmental responsibility and resource conservation. Microorganisms play a pivotal role in this process by facilitating the breakdown of organic matter and the removal of harmful compounds from effluent water. This article explores the diverse roles of microorganisms in aquaculture effluent treatment, including their involvement in nitrogen and phosphorus removal, organic matter decomposition, and pathogen control. Various microbial-based treatment methods, such as biofiltration, microbial mats, and constructed wetlands, are discussed, highlighting their efficiency in reducing pollutants and improving water quality. Furthermore, the potential challenges and prospects of utilizing microorganisms for aquaculture effluent treatment are addressed, emphasizing the importance of research and innovation in developing sustainable solutions.