The present investigation was carried out to evaluate the microbial parameters of Elobeid drinking water supply systems, which comprise of Bara underground water system and the surface rainwater harvesting (RWH) system, during the period from July 2010–June 2011. Four samples from Bara and nine from RWH were collected. The microbial parameters were determined using different microbial techniques. The results showed that the mean total viable bacterial (TVC) and spore-forming bacteria counts in the RWH system were ranged as 80.26-1030.11 and 82.8-3479.8 cfu/ml, respectively and 4.67-110.5 and 0.83- 292.5 cfu/ml, respectively in Bara. Moreover, high counts of coliforms, faecal coliforms; faecal Streptococci, Salmonella, Staphylococci, Clostridia and Cyanobacteria were recorded in the RWH system, particularly during the rainy months (June–September), which not in agreement with international or local standards for drinking water. The predominant bacteria in the two water supply systems were Bacillus (6 species) Proteus mirabilis, Pseudomonas aeruginosa, Pseudomonas maltophilia, Enterobacter gergoviae, Enterobacter alvi, Proteus vulgaris, E. coli, Salmonella choleraesuis, Staphylococcus aureus, Streptococcus faecium and Streptococcus faecalis, in addition to many Cyanobacterial genera: Lyngbya, Microcystis, Oscillatoria, Synechocystis, Anabaena, Leptolyngbya, Dermocarpa, Aphanizomenon, Schizothrix and Phormidium. The presence of those harmful bacteria in water before and after treatment in the RWH system indicated that water treatment measures adopted by the North Kordofan State Water Corporation (coagulation, sand filtration and disinfection by chlorination) do not guarantee acceptable levels of water disinfection. To alleviate these problems, blending of the two water systems and subsequent treatments to reduce microbial load were suggested as recommended point of view.