Aquatic ecosystems, encompassing rivers and lakes, serve as critical habitats supporting diverse microbial communities crucial for ecosystem functioning and human well-being. Seasonal changes in certain environmental factors greatly influence the microbial communities in these aquatic ecosystems. The aim of this research was to evaluate the seasonal variation of bacteria and fungi isolated from rivers and lakes. A total of 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. All the generated data were statistically analysed using SPSS software version 22. A total of two hundred and sixty-six (266) isolates were recovered from the samples. Bacteria isolates represent 241(90.60%) of the total number of microbial isolates compared to the fungi isolates 25 (9.40%). The characteristics of the studied bacteria suggests the identities of the bacteria to be Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Klebsiella pneumoniae and Salmonella Typhi. The characteristics of the fungi colonies represent that of Aspergillus niger, Aspergillus flavus, Candida albicans etc. Our data demonstrated a seasonal variation in the occurrence of bacteria across all sample location with high percentage occurrence recorded for rainy season than dry season although the observed variation was not statistically significant at p-value > 0.05. Various seasonal dependent socioeconomic activities could lead to the depletion of water quality, and thereafter changes the seasonal ecology of the rivers.