Access to adequate supplies of good quality drinking water continues to be limited among many rural and peri-urban communities in Africa, despite several decades of water improvement programmes. The present study investigated water quality at the source and point of consumption among rural and peri-urban communities in northern Sudan. Faecal coliform counts were determined by the membrane filtration technique and geometric mean counts compared in different seasons and among the different communities. Among nomadic pastoralists and riverine villages, both water sources and water stored for consumption had faecal coliform counts grossly in excess of WHO standards, with higher counts at the end of the rainy season. In the peri-urban community on the outskirts of Omdurman, while water quality from the distribution system had faecal coliform counts generally below 10 dl−1, after storage, water was of considerably lower quality, with faecal coliform counts up to 1000 d1−1. The highest counts again occurred in the rainy season. Rates of diarrhoeal disease for Khartoum province were also greatest towards the end of the rainy season. The study has shown that poor quality water continues to be a major risk factor for public health in these communities.