This study was carried out on microalgae attached with sediment and three submerged macrophyte namely, Potamogeton pectinatus (L.), Myriophyllum spicatum (L.) and Najasarmat (H.) during 2006.Mean Chl. a concentrations on biofilm of sediment varied between 18.50 in autumn and 31.73 mg/m² in summer, respectively. Qualitatively, 200 taxa of periphytic microalgae were identified, 73 epipelic taxa and 127 epiphytic algae. Diatoms were the most dominant epipelic algae (> 91%). The pinnate forms of epipelic diatoms(Navicula, Nitzschia, Melosira and Gomphonema spp.) were abundant at the upper lake, while the centric forms (Cyclotella spp.) dominated at the lower one. Similarity index value of epipelic algae showed a weak relationship between the north and the south lakes and disappearance of this relation between the stations of the second lake. Epiphytic algae were represented by Bacillariophyceae (86 taxa), Cyanophyceae (21 taxa), Chlorophyceae (19 taxa) and Dinophyceae (one taxon). The current data revealed that, 71 species were attached with P. pectinatus, 47 with N. armata and 43 species with M. spicatum. Diversity index values of epiphytic diatoms were generally higher than green and blue green algae. Generally, the epiphytic algae are usually more abundant compared to epipelic microalgae inhabiting Wadi El-Rayian Lakes.