Landsat 7 Thematic Mapper data of March, 25, 2000 based on GIS were used to track and monitor of phytoplankton blooms in Lake Nasser - Toshka area. Principal component analysis (PCA) and the maximum likelihood classification algorithms wereapplied to separate different land use types. The spatial data analysis together with the ground reference studies weresignificantly revealed the distribution pattern of bloom - forming cyanobacteria of Microcystis aeruginosa f. flos aquae (wittr.) Elenk., Aphanizomenon flos-aquae (Lemm.) Ralfs ex Borb. et Flah. and detected the spectral signatures of the euhydrophytes intermingled with phytoplankton. The spring and summer blooming of cyanobacteria was correlated with physico-chemical characteristics of water. Ecologically, the cyanobacterial species have adverse effects through producing toxic compounds. In conclusion, this paper gives an early warning on the spatial distribution of toxic cyanobacterial species which will be used as the first trial inventory for future multitemporal studies.