Water samples for bacterial analyses were taken, when possible, at 41 sites in Lebanon and Syria in the El-Kabir River watershed. Samples were analysed for total coliform (TC), faecal coliform (FC) and faecal streptococcus. The Lebanese samples also were analysed for the presence of sulphate-reducing bacteria. The TC and FC concentrations were extremely high throughout the watershed, rendering the water unfit for any human uses. The origin of the bacteria is the untreated sewage waste from the numerous settlements situated throughout the watershed. This primary origin is supported by high ratios of FC/faecal streptococcus, although impacts from animal wastes also were observed. The bacterial levels were higher in summer than in winter, indicating a high winter river flow that dilutes a relatively constant source of human sewage discharged to the system. Spring waters also exhibited elevated levels of bacteria, implicating surface land use and waste disposal practices upstream of the springs. The data clearly shows that human health is at a high risk and that strategies for improving water quality and protecting spring water must be expeditiously implemented.