Aquaculture has become the fastest-growing food production sector, with steady growth in recent years, and is a key player in the national development and poverty reduction plans of most nations. Nevertheless, aquaculture progress at high rates has brought fears regarding pond effluents, which could harm aquatic ecosystems locally through the elevation of nutrient discharge. Sludge buildup, which consists mainly of excess feed and organic matter that has decomposed, is a serious environmental concern. Effluents need to be properly treated before discharge from culture ponds to minimize such impacts. Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gases, industrial effluents, etc., in natural or artificial settings. Bioremediation, a chemical-free process that is environmental friendly, has attracted the attention of researchers as an effective means of organic waste management. This chapter delivers into the promise of helpful bacteria to bioremediate aquaculture waste and simultaneously confronts the toxic elements of aquaculture effluent.