Aquaculture, driven by increasing demands for animal proteins and fats, faces multifaceted challenges stemming from environmental factors such as climate change and pollution, alongside issues like disease susceptibility and limited therapeutic tools. However, the emergence of nanotechnology (NNT) offers a promising solution across various aquaculture domains. Nano-enhanced feed has been shown to improve fish growth rates, while nanomaterials are reducing the treatment economy by effectively eliminating contaminants. Genetic manipulation methods combined with nanobiotechnology have revolutionized fish ancestry studies, with advancements such as nanosensors and DNA-based vaccines significantly impacting fish life and immune systems. Moreover, nanotechnology plays a crucial role in enhancing fish processing, enabling sterile packaging and precise flavoring. Utilizing fishery waste through bio-nano-engineering and green nanoparticles offers new post-harvesting practices. Despite ongoing exploration, NNT presents versatile applications, prospects, and challenges in aquaculture, as detailed in this review. This paper provides an in-depth analysis of current trends, challenges, and prospects of NNT applications in aquaculture.