Surveillance of Emerging Zoonotic Pathogens in Water Systems: Tools and Frameworks for a One Health World

Increased land-use change, climate variability, urbanization, and intense human–animal interactions are reshaping the global view of zoonotic disease emergence, with water systems increasingly acting as final sink for spillover, transmission, and early detection. Water systems, including wastewater, surface waters, and wetlands integrate biological signals from humans, livestock, wildlife, and ecosystems, yet their role within One Health frameworks remains unevenly integrated. This review synthesizes current evidence on the role of aquatic systems in the emergence, persistence, detection, and control of zoonotic pathogens across human-animal-environment interfaces. The reviewed literature demonstrates that water systems consistently capture signals from diverse zoonotic agents, including enteric protozoa ( Cryptosporidium , Giardia ), bacterial pathogens ( Vibrio cholerae , Leptospira spp .), viral threats ( SARS-CoV-2 , Influenza A , West Nile virus , mpox ), and antimicrobial resistance genes, often preceding or complementing clinical detection. Advances in molecular diagnostics, including multiplex and digital PCR, high-throughput sequencing, and wastewater-based epidemiology, have substantially improved sensitivity, source attribution, and genomic resolution, enabling population-level monitoring and early outbreak detection. Case studies across high-, middle-, and low-income settings illustrate that water surveillance can identify wildlife and livestock reservoirs, track pathogen persistence and seasonal dynamics, and reveal gaps in treatment efficacy, particularly for resistant organisms and environmentally persistent pathogens. However, significant challenges remain, including variability in sampling strategies, limited sequencing capacity in resource-constrained regions, incomplete wildlife monitoring, insufficient sequencing and bioinformatics capacity, and weak integration of environmental data with clinical and veterinary surveillance systems. Ethical, governance, and data-sharing barriers further constrain implementation. The evidence highlights water systems as indispensable components of integrated zoonotic surveillance. Strengthening water-based monitoring through coordinated One Health approaches, supported by harmonized methods, cross-sectoral data platforms, and climate-informed risk models, will be essential for improving early detection, preparedness, and prevention of future zoonotic threats.