Water quality has been linked to health outcomes across the world. This study evaluated the physico-chemical and bacteriological quality of drinking water supplied by the municipality from source to the point of use at Thulamela municipality, Limpopo Province, South Africa; assessed the community practices regarding collection and storage of water and determined the human health risks associated with consumption of the water. Assessment of water quality was carried out on 114 samples. Questionnaires were used to determine the community’s practices of water transportation from source to the point-of-use and storage activities. Many of the households reported constant water supply interruptions and the majority (92.2%) do not treat their water before use. While E. coli and total coliform were not detected in the water samples at source (dam), most of the samples from the street taps and at the point of use (household storage containers) were found to be contaminated with high levels of E. coli and total coliform. The levels of E. coli and total coliform detected during the wet season were higher than the levels detected during the dry season. Trace metals’ levels in the drinking water samples were within permissible range of both the South African National Standards and World Health Organisation. The calculated non-carcinogenic effects using hazard quotient toxicity potential and cumulative hazard index of drinking water through ingestion and dermal pathways were less than unity, implying that consumption of the water could pose no significant non-carcinogenic health risk. Intermittent interruption in municipal water supply and certain water transportation and storage practices by community members increase the risk of water contamination. We recommend a more consistent supply of treated municipal water in Limpopo province and training of residents on hygienic practices of transportation and storage of drinking water from the source to the point of use.