Aquaculture is one of the fastest-growing food production sectors in the world, playing a crucial role in fulfilling the increased demand for animal protein requirements and ensuring future food security. To meet the challenge of global food security, production and productivity have increased multifold due to intensification in the aquaculture systems. Disease prevalence, environmental degradation and chemical contamination are major factors hindering the outcomes. In this regard, nanotechnology has opened new avenues for its application to cope with these challenges in aquaculture and increase production, efficiency and sustainability. Nanotechnology has a significant role to play in improving the efficiency of the aquaculture system. It has an array of applications in fish health management, viz., as an antimicrobial agent for disinfection, treatment of water pollutants, delivery of vaccines, drugs, nutraceuticals and dietary supplements, as nanosensors for pathogen detection and control of biofouling agents, etc. This chapter discusses the various aspects of nanotechnology in aquatic animal health management.