Three different rivers in Ogun and Ondo states were investigated for both micro and macro-biota of the water bodies. Several physical and chemical properties of these rivers were determined. The pH value of the studied water bodies was essentially neutral with salinity values between 0.02 -4.0‰. Microalgae communities were represented by three divisions: Cyanophyta, Bacillariophyta and Chlorophyta at Oluwa and Ifara Rivers (Ondo state), while at Ibefun River (Ogun state), five divisions: Cyanophyta, Bacillariophyta, Chlorophyta, Euglenophyta and Pyrrhophyta were identified. Diatoms dominated these water bodies, with Navicula radiosa Kutz. at Ifara River, Fragilaria sp. in Oluwa River, while out of 90 algal taxa identified in Ibefun river, 64 were diatoms species belonging to 26 genera, with Melosira sp. and Synedra sp. recording the highest numbers of cell count. Dinoflagellates recorded only Peridinium sp. while Phacus orbicularis Hubner and Trachelomonas sp. dominated the euglenoids. For the zooplankton composition at Ibefun, rotifers (75.95%) were represented by Brachionus sp., which recorded 62.03%, and Gastropus sp. with 13.92% of the total zooplankton, thus dominated the spectrum, while the copepod recorded 22.78% of the total organisms, with Copilia sp. and Euchirella sp. having 8.86% each. The macrobenthic invertebrates were represented by 3 taxa, belonging to 3 groups, with the dominant group Insecta accounted for 57% of the total individuals (7 individuals/m 2 ), while Oligochaeta and Hirudinea accounted for 29% and 14% respectively of the total individuals at Oluwa and Ifara Rivers. At Ibefun River, the macrobenthic invertebrates were represented by 5 taxa, belonging to 3 groups, Bivalves, Oligochaeta and Insecta, with bivalves being the dominant group (51.7% of the total individuals, as 64 individuals/m 2 ), while Oligochaeta and Insecta accounted for 26.6% and 21.9% respectively of the total individuals. The dominant taxon, Macoma cumana, accounted for 42.2%. A total of seventeen (17) finfish and shellfish species comprised of thirteen (13) finfish and four (4) shellfish species were recorded, being representative of freshwater and brackish water species; Clarias anguillaris (Clariidae), Tilapia zilli (Cichlidae), Chrysichthys nigrodigitatus (Bagridae), Alestes spp. and Macrobrachium vollenhovenii (Palaemonidae) were the most common species observed.