This paper investigates the contamination of floodwaters in the urban center of Can Tho city, Vietnam. We sampled water from sewers, surface water bodies, and flood, before, during, and after specific flooding events. Total nucleic acid was extracted from the samples and subjected to a quantitative polymerase chain reaction (qPCR) to detect specific enteric pathogens. The difference between pathogen concentrations in floodwater and sewer water was compared by using the Mann Whitney U test. Correlations between the different pathogens were determined using the non-parametric Spearman test. E. coli and Rotavirus-A were the most prevalent pathogens in floodwater. We observed a weak association between E. coli and Rotavirus in flood-related waters (r < 0.5). Floodwater quality showed no difference to sewer water quality in terms of the E. coli and Rotavirus A concentrations (p > 0.05). Our results indicate that floodwater poses a significant urban public health risk due to the presence of enteric pathogens.