The present investigation aims to study the dynamics of the harmful bloom-forming cyanobacterium Microcystis aeruginosa with its Cyanophage Ma-LMM01 in the River Nile ecosystem. Two freshwater samples in the Damietta branch of the River Nile represented the inlet and the outlet of a drinking water treatment plant were assessed according to a number of physicochemical and biological parameters. The total dissolved hepatotoxin microcystins in the raw and potable water were tested using the ELISA technique. Quantitative analysis of the 16S rRNA, mcyA, and g91genes was done in order to estimate microcystin-producing organisms and the Ma-LMM01 cyanophage. The results showed a high growth reached bloom-forming of Microcystis aeruginosa in the raw water while the treated one showed a vanishing in the number of Microcystis aeruginosa. A high concentration of microcystins was detected during the study period with the highest concentration of 4.4 µg. L^-1 was recorded in the raw water sample during July.  The sequencing result of the amplification products of the g91 geneproves the presence of cyanophages but generally in a lysogenic state. The results obtained from this study revealed the presence of cyanophage Ma-LMM01 concomitantly with the presence of Microcystis aeruginosa bloom without having a high lytic effect.