Aim: The microbiological quality of Ikpoba River, Benin City-Nigeria and the surrounding borehole waters was investigated to assess the extent of pollution from Guinness Nigeria Plc, Benin City. Methodology: Microbiological parameters analyzed were total bacterial, fungal and coliform counts, and identification for indicator organisms. Results: For river water samples (RW1-RW4), mean total viable aerobic bacterial, fungal and coliform counts ranged from 0.06x108 to 35.0x108 CFU/mL, 0.6x104 to 2.5x104 CFU/mL, and 0.006x106 to 2.3x106 CFU/mL respectively; and for borehole water samples (BH1-BH5), mean counts ranged from 1.3x104 to 3.3x104 CFU/mL for bacteria, 4.0x10 to 8.2x10 CFU/mL for fungi, and 0 to 6.1x102 CFU/mL for coliforms. Only BH1 and BH5 showed the absence of coliforms.... Conclusion: From the results of this study, it was observed that the effluent discharge from Guinness Nigeria Plc may not totally be responsible for the microbial contamination of the Ikpoba River and the surrounding borehole waters, as other sources of contamination, especially from human activities, were noticed. It is therefore important that governments and concerned institutions put measures in place to remove the sources of contamination in water bodies that supply locals with water for household use. Industrial effluent also, should be effectively treated before they are discharged into the water body and industries should strictly adhere to the standards and guidelines specified by various water and environment regulating bodies.