Aquaculture represents the fastest growing primary sector and supports increasing demand for animal proteins and fats. In contemporary times, its prolific growth potential has been challenged by multiple abiotic stressors, including climate change, pollution, water scarcity, etc. Alternatively, increased disease susceptibility, the emergence of new pathogens, and low efficacy of conventional theragnostic tools appear to be the major bottlenecks in tackling sustainability. Nanotechnology has emerged as an innovative and efficacious tool in the field of fish nutrition, biotechnology, genetics, reproduction, pathology and sustaining environmental quality etc. The application of nano-elements enriched feed has deliberately enhanced the fish growth. Emerging nano-materials are currently applied in aquatic system to reduce treatment costs by wiping off pollutants. Genetically manipulated techniques, in combination with nano-biotechnology has revolutionized fish genetics research. Newer usages of nano-sensors, DNA nano-vaccines, nano-inspired genes, and drug delivery systems have reformed the fish health, reproduction, and immune system. In addition, nanotechnology are currently being employed in fish processing industry for sterile packaging, exact flavor, and quality. Optimum utilization of fishery wastes using bio-nano-engineering technique and implication of green nanoparticles have ushered a novel post-harvesting era. Dimensions of applied nanotechnology in the aquatic system are still on the verge of initiation. The present review aimed to provide an in-depth screening into the novel and versatile applications of nanotechnology in aquaculture alongwith its prospects and challenges.