Aquatic animal diseases form the most significant limiting factor in aquaculture production. As diseases in aquaculture result from a complex interaction between host, pathogen, environment and anthropogenic factors, and complete elimination of disease risk is almost impossible, a science-based health management strategy will be the cornerstone of sustainable aquaculture development. Addressing current challenges such as disease outbreaks, antimicrobial resistance and climate change requires a multidisciplinary approach combining strict biosecurity, stocking quality seed, using appropriate feed for complete nutrition, health monitoring and disease surveillance, and therapeutic and prophylactic strategies. The understanding of the concept of pathobiome and disease development processes in recent years has further strengthened health management strategies in aquaculture. Precise diagnosis plays a crucial role in health management, specifically in the stock maintenance and administration of appropriate therapeutic measures. Strict biosecurity and regulatory mechanisms can control the transboundary movements of infectious agents and curtail the indiscriminate use of drugs and chemicals. Future advancements in digital technologies, AI-based diagnosis and disease prediction, effective vaccines and genomic tools offer better ways to improve aquaculture health management.