Abstract: The aim of this study was to evaluate bacterial quality and pathogenic organism presence in the Nile water (Blue, White and Main River Nile) as sources of drinking water in Sudan. The bacterial genera were isolated and identified using microbiological and biochemical method of evaluation. The most predominant aerobic microflora genera and species found in the Nile waters were Bacillus, Aerococcus, Micrococcus, Pseudomonas, Staphylococcus, Actinomycetes, Aeromonas and Streptococcus. Only two genera were identified to their species, Bacillus (B. cereus, B. subtilis, B. licheniformis and B. Penibacillus) and Streptococcus (S. faecalis, S. faecium). The most frequent coliforms isolated were Escherichia coli, Enterobacter aerogenes, Enterobacter cloacae, Enterobacter agglomerans, Klebsiella oxytoca, Klebsiella planticola, Serratia spp. and Citrobacter spp. The results of bacterial genera isolated in this study indicate that, the Nile water was potentially contaminated with the pathogenic bacteria and therefore, presence of Escherichia coli could be public health risk.