Algal mats and scum were removed monthly (Jan. 2004-Dec.2004) from three tanks walls (oxidation, settling and effluent tanks) of tertiary sewage water treatment plant at El-Katameya city near Cairo. Phytobenthic algae were not detected in the collector tank during the annual course of the present investigation, thus it was examined only in the other three tanks of the sewage water treatment system. Phytobenthos community was represented by 120 species in 47 genera belonging to 4 classes namely, Cyanophyceae (65 species), Chlorophyceae (24 species), Bacillariophyceae (26 species) and Euglenophyceae (2 species). Among the dominant phytobenthos species were Oscillatoria amphigranulate, Oedogonium capillare, Synedra ulna and Nitzschia obtusa v. vulgaris. The increase in nitrate concentration during the nitrification phase of the biological activated sludge treatment process was found to be the main factor contributing to the high growth of benthic algae in the treatment system, decreasing nitrification phase time and injected oxygen set point reduced nitrate levels which in turn resulted in the full disappearance of benthic algae from the treatment system. The study proved that decreasing the nitrification phase time from 20 minutes/hour to 10 minutes/hour and the injected oxygen set point from 1.5 mg/L to 1.0 mg/L was ideal for the full disappearance of benthic algae from the treatment system. The treatment system was operated under such conditions for two months (October and November 2005).