Vol. 9, Issue 11, Part F (2025)

Freshwater aquaculture is a critical component of global food security, yet its sustainability is threatened by infectious disease outbreaks exacerbated by intensive farming practices. Traditional chemical therapeutics, while initially effective, pose significant environmental and safety concerns, including non-target toxicity, pathogen resistance, and regulatory restrictions. This comprehensive review synthesizes recent advances in sustainable disease management strategies, emphasizing the role of omics technologies in elucidating host-pathogen interactions, the application of green therapeutics and immunostimulants, and the emerging potential of nanotechnology. Through a systematic analysis of 40 omics-based studies, we highlight key bacterial, viral, and parasitic pathogens that affect major freshwater species and detail the molecular mechanisms underlying disease progression and immunity. We further explore how nanotechnology—particularly nano-vaccines, selenium nanoparticles, and chitosan-based nanocomposites—offers innovative solutions for targeted therapy, enhanced nutrition, and environmental remediation. The integration of these approaches within a proactive health management framework is essential for advancing ecological safety, host resilience, and economic viability in aquaculture. We conclude that the future of sustainable aquaculture depends on the synergistic application of omics-driven insights, green chemistry, and nano-enabled technologies, supported by global cooperation in biosecurity and policy implementation.