Heavy metals are among the most harmful environmental pollutants and are released into aquatic ecosystems mainly through industrial activities, leading to severe water pollution. Nearly 70% of industrial effluents are discharged into water bodies without proper treatment, contaminating usable water sources. Toxic metals such as cadmium, nickel, arsenic, and lead adversely affect fish growth, reproduction, and physiology, posing a serious threat to the sustainable development of aquaculture. Various strategies, including microbe-mediated synthesis of nanomaterials and biofunctionalized processes, are being explored to develop sustainable and efficient bioremediation techniques for removing heavy metals, hydrocarbons, and other chemicals. The nanoparticles synthesis by microorganisms (Bacillus sp., Terichoderma sp., Fucus vesiculosus) has gained significant interest due to their potential to synthesize nanoparticles in various sizes, shape, and composition with different physico-chemical properties. Microbes can be widely applied for nanoparticles production due to easy handling and processing, requirement of low-cost medium such as agro-wastes, simple scaling up, economic viability with the ability of adsorbing and reducing metal ions into nanoparticles through metabolic processes. Nano-bioremediation, a combination of bioremediation and nanotechnology is a competent way to remove contaminants from aquatic systems as it is a non-toxic, cost-effective, and less time-consuming approach. The nanomaterials such as graphene oxide, carbon nanotubes, metal oxides, carbon-based NPs, zero-valent metal-based NPs, polymer-based adsorbents, and other nano-combinations, which were used for remediation of heavy metals from aquatics.