The microalgal communities and related physico-chemical properties of some agricultural drainage at Minia, Egypt as well as, the qualitative and quantitative algal composition were seasonally studied. In total, 151 algal species were identified during the study. Bacillariophyceae was the most dominant algal group during the four seasons, followed by Chlorophyceae, Cyanophyceae, Euglenophyceae, Charophyceae and Dinophyceae. Among Bacillariophyceae, Cyclotella striata was the most abundant species, Scenedesmus quadricauda from Chlorophyceae, Oscillatoria limosa from Cyanophyceae, Euglena proxima from Euglenophyceae, Staurastrum sp. from Charophyceae and Peridinium lomnicki from Dinophyceae. The maximum algal biomass was recorded at site 1 in autumn (827.7µg/L); and the minimum value was recorded at site 4 in winter (26.7µg/L). Seven diversity indices were obtained that comprise Margalef's Index, Shannon-Wiener Diversity, Pielou's Evenness, Fisher's Index, Simpson Dominance Index, Simpson's Diversity Index and Berger-Parker Index. Water temperature, total alkalinity, chloride and phosphate were the most effective parameters affecting structure of microalgae during the different seasons.