This study was carried seasonally at WadiEl-RayianLakes during 2006. Total phytoplankton densities in the upper WadiEl-RayianLake were 4.8 fold higher than the lower lake..Their major peak was recorded in winter and the minor in summer.Cyanophyceae and Chlorophyceae were dominated in the first lake, while Bacillariophyceae and Dinophyceae in the second lake. Cyanobacteria as Microcystis flos-aquae, Microcystis aeruginosa  and Lyngbya limnetica blooms in the first lake during winter. The algal species in the first lake are mainly freshwater forms  while some of those found in the second lake are brackish and marine forms such as Chaetocerous similes Cleve, Prorocentrum micans Ehr., Prorocentrum apora Schiller and. Hermesium adriaticum Zacch which also new record. Diversity index values indicate instability of Wadi El-Rayian depression, its values less than 1 and not exceeding 3. Similarity index exhibited a close relationship between the middle and the southernmost stations of both lakes. According to Carlson's trophic index, the first reservoir is classified as mesotrophic to eutrophic, while the second lake ranged from oligotrophic to eutrophic. Ammonium concentrations were much higher than the oxidized nitrogen in the two lakes under investigations. The trophic status, increased over time through continuous watershed management neighboring this depression.