The research on the algae of the Lower Euphrates Basin of the South East Anatolian Region was done between November 2001 and August 2003 at twenty one stations each, on four different habitats (plankton, epipelon, epifithon, epilithon). Due to the density level of species, Cyanobacteria, Bacillariophyta and Chlorophycophyta were conspicous. A bloom of Microcystis aeruginosa was observed in Ataturk and Halfeti Reservoirs in September 2002. In the same period, Cyclotella ocellata, in May 2003 Cyclostephanos dubius, and in August the same year. It could be said that Ceratium hirundinella species were close to bloom level. High density diatoms were found more in plankton. Species such as Oscillatoria spp., Spirogyra spp. and Lyngbya spp. were observed to be more wide-spread than the others. Species such as Oscillatoria spp., Leiblenia epiphytica and Phormidium mucicola increased in abundance in February and September in running waters. Within these months, water temperature in the region ranged between 18-22 degrees C. According to some chemical and biological data, the basin was mesotrophic while some streams with sewage inputs, were observed to have eutrophic characteristics.