Water security and safety is of vital concern in arid and semiarid regions of Kenya. Potable water accessibility and supply is limited due to fluctuating climatic conditions and environmental pollution that lower the wholesomeness of most water sources. The aim of this study was to establish the suitability of these water sources for drinking and use in industrial food processing by the small and medium enterprises (SME's). The aim of this study was to establish suitability of these water sources for drinking and use in industrial food processing by the small and medium enterprises (SME's). A total of 60 surface and ground water sources samples were purposively collected aseptically from the four administrative units (Ngare Mara, LMD, Leparua, and Wabera) of Isiolo County. ISO 16649-3, 688-2, 7937, 9308-1, and 18744 were used for enumeration of E.coli, Staphylococcus aureus, Clostridium pafringens, Coliforms, and cysts. Highest mean Clostridium pafringens counts in ground and surface water were 1452 Cfu/ml and 3421 Cfu/ml, respectively. Mean Staphylococcus aureus counts were 740 Cfu/ml and 1333 Cfu/ml in surface water and ground water, respectively. Escherichia coli and Coliforms contamination accounted for 29.88 % and 88.2 %, respectively. Microbial counts in the water sources differed significantly (p≤0.05). Total coliforms had a significant negative relationship (r = -0.76) with residual chlorine. Ground and surface water sources were highly contaminated with microorganism to levels regarded as unsafe by the Kenyan and WHO standards for potable water. Point-of-use water disinfection is thus necessary.