This study assessed the occurrence of endotoxins, cyanobacteria and enterobacteria in untreated drinking water stored in domestic water containers by rural households in South Africa. Endotoxins, cyanobacteria, total coliforms and Escherichia coli were measured in the following numbers and ranges in container-water samples: 4–54 μg l−1, 69–64,505 cells ml−1, 9,000–280,000 CFU/100 ml and 90–1,100 CFU/100 ml, respectively, in source water and 0.23–24.7 μg l−1, 1–501,187 cells ml−1, 25–1,584,893 CFU/100 ml and 1–25,118 CFU/100 ml, respectively, in water from containers. The concentrations of these contaminants in water often exceeded guidelines. Container type, especially those that permit light into the vessel, played a significant role in the occurrence of these contaminants. Limited guidelines, as well as the absence of health evidence, make it uncertain whether the high levels of endotoxins in the containerised drinking water could cause a health effect in healthy persons. Most importantly, in the context of exposure to endotoxins potentially derived from high levels of cyanobacteria and enterobacteria such as coliforms in the water, a case is made for possible health effects in immune-compromised individuals exposed to water containing endotoxins and the bacteria that potentially produce it.