Raw water samples of two drinking water treatment plants (named New Mansoura and Bilqas stations) were collected for a full annual cycle. Analyses of total soluble inorganic N, dissolved reactive phosphorus (DRP) and Total dissolved phosphorus (TDP) were carried out. Qualitative and quantitative analysis of Cyanoprokaryotes and photosynthetic pigments of phytoplankton were investigated. Total microcystins of raw water supply and potable water were seasonally analyzed using ELISA. Seven Cyanobprokaryotes species were isolated, cultured under lab conditions and biomass contents of microcystin–LR and -YR were analyzed using HPLC. Physico-chemical characteristics and photosynthetic pigments displayed pronounced periodic variations. Species composition and abundance of Cyanoprokaryotes exhibited marked seasonal variation during the period of study. Cyanoprokaryotes biovolume peaked in summer at New Mansoura (214.3mm³m^-3) and Bilqas (161.3 mm³m^-3) water treatment stations. The minimum mean biovolume of 25.2 and 30.8 mm³m^-3 were recorded in winter at New Mansoura and in autumn at Bilqas station, respectively. Total microcystins in raw water maintained seasonal variations. Microcystins values were 2.2 and 2.0 µg l^-1 during summer at Bilqas and New Mansoura respectively. Theses values of 1µg l^-1 exceeding the WHO guidelines. Total microcystins of potable water were below the WHO guideline except in summer at New Mansoura (1.2µg l^-1). Microcystins in biomass of different species of Cyanoprokaryotes varied between 3.0 mg g^-1 (8% LR and 92%YR) and 0.3 mg g^-1 (100% LR) recorded for Anabaena oryzae and Anabaena khannae, respectively.