Animal manure has been traditionally used to fertilize fish ponds in Vietnam. While this practice effectively reuses agricultural wastes, high concentrations of pathogenic microorganisms in animal manure raise public health concerns. Working in fish ponds and handling of contaminated fish in unhygienic manner were identified as potential factors of occupational risk. Escherichia coli occurred in numbers <103 colony forming units (CFU)/100 mL in irrigation water and <104 CFU/100 mL in fish pond water that uses animal manure. Escherichia coli on tilapia skin in numbers were <103 CFU/100 cm in excreta-based systems and <101 CFU/100 cm in feed-based systems, respectively. The study identified direct use of animal manure as major contributors of the fecal contamination of pond water as well as skin of cultured fish. Estimated risks of enteric infection were 100–1000 times higher than the US Environmental Protection Agency acceptable risk. While these risk values are not likely to accurately predict infection rates in Vietnam, they indicate a potential occupational risk in the long term. Therefore, a need for risk mitigation measures was realized for health protection of future generation in agricultural communities.