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 physicochemical 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 during 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 two lakes included typical groups such as Chlorophyceae, Cyanophyceae, Bacillariophyceae, Cryptophyceae, Dinophyceae, Chrysophyceae, and Euglenophyceae. The green alga was the dominant group, 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. The major peak of phytoplankton density (7684×10 4 Cells L -1 ) was observed during winter, whereas the minor peak was detected during summer (4879×10 4 Cells L -1 ). Cosmarium nitidulum (Brebisson) Ralfs, Dictyosphaerium pulchellum Wood, Oocystis solitaria Wittrock, Gomphosphaeria compacta (Lammermann) Ström, Lyngbya Structure and Biochemical Analysis of Phytoplankton in the Wadi El-Rayan Lakes, El-Fayoum, Egypt 18 limnetica Lemmermann, Microcystis aeruginosa Kützing, Cyclotella meneghiniana Kutz., and Syndra ulna (Nitzsch) Ehr. were the most abundant species identified. More detailed studies on the biochemical structure of phytoplankton are needed to better understand Wadi El-Rayan lakes' response to the many environmental changes.