The aquatic environment especially the rivers and lake within the State of Anambra, Nigeria have been such that serves as avenue for different activities ranging from domestic to religious, agricultural, flood, etc. Thus, its ability to encourage the proliferation of microorganisms. This study was aimed at isolating and identifying bacteria and fungi from rivers and lake located at Anambra Central Senatorial District, Anambra State. Forty-two water samples were collected in triplicates from seven (7) water bodies randomly selected from each town representing the seven (7) Local Government Area in Anambra Central Senatorial District. Bacteria and fungi were isolated from these samples using standard isolation techniques. The isolates were identified phenotypically through morphological, microscopic and biochemical characteristics. A total of two hundred and sixty-six (266) isolates were recovered from them. Bacteria isolates represented 241(90.60%) of the total number of microbial isolates compared to the fungi isolates 25(9.40%). The bacteria isolated were Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Klebsiella pneumoniae and Salmonella Typhi while the fungi isolates were Aspergillus niger, Aspergillus flavus, Candida albicans etc. Bacillus subtilis was observed to be predominant among the bacteria isolates while Candida albicans was predominant among the fungi isolates. In this study, the results established the presence of both bacteria and fungi in varying degrees. The frequency of occurrence of bacteria isolates was significantly higher than the fungi isolate in all the sample locations. This shows that bacteria greatly exceed fungi numerically in all habitat including aquatic habitat as equally reported by most researchers.