Wadi El-Rayan lakes are an important source of irrigation water and fisheries in El-Fayoum Governorate, Egypt. Phytoplankton is an important bioindicator of the chemical and biological changes in natural ecosystems including the Wadi El-Rayan lakes. Seasonal and regional variations lead to concomitant changes in the total protein, carbohydrate, and lipid contents of phytoplankton; such changes affect the nutritional quality of food available in the aquatic system. In the present study, these changes were determined in the phytoplankton of Wadi El-Rayan lakes. The maximum protein (27.95 & 11.36 mgL-1) contents were detected in summer and winter respectively. The maximum carbohydrate content was detected in autumn and winter (1.76 and 1.12 mgL-1 at site 8 and 4 respectively).The maximum lipid content was observed in winter (0.73 mgL-1 at site 6). Phytoplankton density was much higher in the upper lake than in the lower lake. In total, 92 species were identified; the phytoplankton community in the lake included typical groups such as Chlorophyceae, Cyanophyceae, Bacillariophyceae, Cryptophyceae, Dinophyceae, Chrysophyceae, and Euglenophyceae. Green alga was the dominant class, constituting 44.4%–45.0% of the phytoplankton standing crop across seasons. Cyanophyceae (29%–39%), Bacillariophyceae (9.7%–16.1%), and Dinophyceae (4.0%–9.2%) were the next most abundant classes; Cryptophyceae, Chrysophyceae, and Euglenophyceae were rarely found.