The global population is increasing at an elevated speed leading to the expansion of urbanization at the cost of environmental degradation, especially aquatic ecosystem pollution due to the enhanced discharge of wastewater. These aquatic ecosystems are primarily polluted by potentially toxic elements, polyaromatic hydrocarbons, dyes, plastics, pesticides, organic compounds, and molecules present in fertilizers, household wastes, industrial effluents, and sewage discharge. The enhanced deterioration of water bodies has led to the search for natural solutions for a sustainable ecosystem. The utilization of the natural microbial flora of the aquatic ecosystem for remediation, more popularly known as bioremediation, is of global interest because of its cost‐effectiveness and eco‐friendly approach. Bioremediation can be broadly categorized into bacterial remediation, mycoremediation, and phytoremediation and is more commonly studied for soil pollution. However, in this review, we discuss bioremediation techniques and mechanisms with respect to water pollution. Aquatic microbes utilize the toxic components present in wastewater as a substrate for their own metabolism by acting as a biologically active methylator or by chemical alteration of the toxicants into less harmful products, thus degrading the toxic environmental pollutants into nontoxic products thereby eliminating their detrimental effects. Microalgae used in phytoremediation also help to elevate the dissolved oxygen level in the aquatic ecosystem thereby reducing the probability of eutrophication. This review represents the study of diverse pollutants remediation and a method involving microbial consortia in a bioreactor for optimum efficacy at minimum cost.