Aquatic products play a crucial role in fulfilling the growing demand of the world’s population for food and provide essential health benefits owing to their high protein and omega-3 fatty acid concentrations that are often lacking in land-based diets. The rapid expansion of aquaculture as a burgeoning food production system has resulted in considerable food safety challenges, particularly concerning the presence of intrinsic toxins (e.g., marine toxins), environmental pollutants (e.g., heavy metals, microplastics, and pathogens), and regulatory issues. Notably, China’s maritime renaissance, which is reshaping the nation’s approach to food security and dietary structures, necessitates urgent solutions owing to its impact on one-fifth of the global population. In response to these pressing challenges, nanostructures have recently been investigated as promising tools for the detection and elimination of hazardous contaminants in aquaculture. Because of their large surface areas and adjustable physicochemical properties, nanostructures can be engineered with antibodies, aptamers, and functional ligands to function as indicators, signal amplifiers, photocatalysts, and separation tools across a wide range of targeted applications. This review presents the latest advancements in the application of nanostructures for safeguarding aquacultural environments and food products. It begins with an overview of aquacultural safety challenges and currently established solutions, followed by a comprehensive analysis of how diverse nanostructures are being utilized for the detection and elimination of hazardous substances from aquacultural systems and products. The review also presents a discussion on the integration of nanostructures into existing aquaculture practices, emphasizing the potential of nanostructures in revolutionizing hazard management by providing rapid, sensitive, and sustainable solutions. Finally, future perspectives on the integration of nanostructures for enhancing aquaculture safety are presented. By addressing both current challenges and future directions, this review underscores the transformative impact of nanostructures in fostering safer and more sustainable aquaculture, contributing to the advancement of global food security.