Water is one of the basic necessities for sustenance of life, and its impact nearly in all areas of life. Diseases related to contamination of drinking water constitute a major burden on human health. In resource-poor and low-population-density areas, on-site sanitation is preferred to off-site sanitation and groundwater is the main source of water for domestic uses. Given the widespread use of groundwater for domestic purposes in rural areas, maintaining groundwater quality is a critical livelihood intervention. This study assessed impacts of pit latrines on groundwater quality in Nguru town, Local Government Area of Yobe State. Water Samples from boreholes, hand pumps and wells were collected from Hausari, Bulabulin, Tsohon Nguru, Sabon gari, and Garbi communities of Nguru town of Yobe State. Parameters analysed were total and faecal coliforms. The number of Total faecal coliforms as well as E. coli of all the samples exceeded the recommended value of 0 CFU/100 ml by WHO guidelines for a good quality for drinking water. Results indicated that significant association existed between distances from water source to the nearest pit latrine and the bacteriological loads in the water samples.