This study was conducted to estimate the distribution of phytoplankton, zooplankton and their correlation with physico-chemical conditions of water for White Nile, Blue Nile and River Nile, April – May 2022. Some of the important physico-chemical factors of the research stations have been analyzed and the water temperature (°C) were (22.00±1.00, 21.00±0.00 and 21.00±0.00), pH (8.47±0.31, 7.6.00±0.35 and 8.07±0.12) and Transperancy (cm) (34.67±11.06, 85.33±4.16 and 47.00±8.54) for White Nile, Blue Nile and River Nile respectivley. The results revealed that there are 18 species of phytoplankton and 18 species of zooplankton were recorded from all the stations. Among these Bacillariophyceae was the most dominant class in phytoplankton 5 genus, followed by 4 genus Chlorophyceae, 3 genus Cyanophyceae, 3 genus Zygnematophyceae, 2 genus Xanthophyceae and 1 genus Coscinodiscophyceae. While zooplankton, 18 different genera, the genus are represented by 6 genus Rotifera, 2 genus for (Crustacea, Rhizopoda, Lobosea and Eurotatoria), 1 genus for (Adenophorea, Phylactolemata, Secernetea and Ciliata). Statistically, phytoplankton showed significat result with zooplankton (r2 = 0.81) and with water temperature and PO4 (r2 =0.43); non-significant different with transperancy (r2 = 0.01); for zooplankton the results showed that the positive relation between zooplankton and turbidity (r2 =0.27) and non-significat with other parameters.