Changes in phytoplankton density and its relation to physico-chemical nature of the River Nile water were monitored from March 2010 to February 2011 from six sampling sites along the River Nile at Qena, Governorate, Egypt. Physico-chemical parameters: temperature, pH, DO, COD, turbidity and nutrients were measured. Eighty three species have identified during the study belong to five divisions of phytoplankton. Chlorophyta was the predominant group by 36 species followed by Bacillariophyta (diatoms) (33sp.), Cyanophyta (11sp.), Dinophyta (2sp.) and Euglenophyta (1sp.). Phytoplankton density ranged from 2597 to 5227 org. ml^-1 along the study period. Also, chlorophyll a content as indicator of algal growth and trophic state are ranged between 2.31 and 26.05 µg L^-1 along the study period.Statistical analysis showed that positive correlation of total algal counts with pH, turbidity, DO and Chl.a.Furthermore, a pronounced correlation was detected between silica concentration and diatoms count.