Abstract
Waterborne pathogens, primarily introduced through agricultural and urban runoff, pose significant threats to public health and water quality. This review examines the mechanisms of pathogen contamination in both surface water and groundwater, focusing on the role of surface runoff induced by rainfall, the impact of agricultural and urban practices, and the resulting microbial contamination of water sources. We explore seasonal and regional trends in pathogen loads, which are influenced by climatic factors, land use, and sanitation infrastructure. Detection methods are discussed, ranging from traditional culturing techniques to advanced approaches like polymerase chain reaction (PCR) and metagenomics. PCR enables rapid, sensitive pathogen detection in water (1–10 CFU/mL) but requires trained personnel and cannot distinguish live from dead cells. Metagenomics provides broad microbial profiling but is less sensitive (~10⁴ CFU/mL), costly, and suited for research. PCR is ideal for field use, while metagenomics aids in comprehensive surveillance. Combining qPCR with culturing enhances detection accuracy. Key challenges in pathogen detection include cost, technical demands, and knowledge gaps about pathogen persistence and transport dynamics. Proactive strategies, including integrated water management, climate-resilient practices, and capacity building for pathogen detection, are proposed to mitigate contamination risks. By combining sustainable agricultural practices, green infrastructure, and climate predictions, these strategies aim to reduce pathogen loads and improve water quality. This review emphasizes the need for continued research, innovative detection technologies, and international collaboration to safeguard water resources and protect public health from the risks posed by waterborne pathogens.

Key words: Waterborne pathogens, Runoff contamination, Pathogen detection, Agricultural runoff, Climate resilience