The present investigation concerned with the study of the algal flora from four different regions of Qaroun Lake. Phytoplankton and Phyto-benthos materials were collected during August 2019. Physical and chemical characters of water at the investigated region of the lake were studied, a total of 23 microalgal species were identified related to Cyanophyta with 10 species, 8 species to Chlorophyta, 4 species for Bacillariophyta and Euglenophyta with one species. The physico-chemical characteristics of water and soils in relation to algal distribution have also been considered. Analyze the possibility of growing microalgae Scenedesmus quadricaudain wastewater as a potential candidate for biodiesel production. Fatty acid composition and the effect of sewage water on ultrastructure of Scenedesmus quadricauda by using the Transmission Electron Microscope were investigated revealed drastic changes in the overall ultrastructure such as the chloroplast separated far from the wall, accumulation of starch and the pyrenoid disappeared. These responses of Scenedesmus quadricauda indicated their tolerance of waste water