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Diarrheal diseases often attributable to poor sanitary conditions and fecal contamination of drinking water remain a leading cause of mortality for children younger than five years. Water contaminated with human faeces, for example from municipal sewage, septic tanks and latrines, is of particular concern. Animal faeces also contain microorganisms that can cause diarrhea. Kakamega County in Kenya has a diarrhea prevalence rate of 20.2%, which is the highest in the country; a good proportion of these cases are believed to be water borne. This study was designed to determine fecal coliform levels in water samples collected from watering points along the upper reaches of River Isiukhu in Kakamega County, Kenya. Fifty-four samples were collected between August and October 2015 from nine sampling points, comprising springs and watering points along the river. Water samples were filtered on nitrocellulose filters by vacuum filtration; fecal coliform counts were conducted using membrane filters cultured on mFC agar to establish contamination levels. The results indicated that counts ranged from 200 cfu/100 ml – 1450 cfu/100 ml in river sampling points and ranged from 0 cfu/100 ml – 44 cfu/100 ml in springs sampling points. The fecal coliform counts for River Isiukhu and most springs surrounding it exceeded the WHO recommended drinking water coliform (or E. coli) count value of 0 cfu/100 ml indicating that water from the upper reaches of River Isiukhu and springs is not fit for drinking before treatment, especially during the wet seasons, based on WHO drinking water standards.