Wadi El-Raiyan lakes lie in the lowest part of El-Fayom Depression in the Western Desert of Egypt. The present investigation deals with the seasonal fluctuation of physico-chemical characteristics and primary productivity of Wadi El-Raiyan-Lakes. The result showed that the water temperature ranged from 13.9 to 30.8 °C and follows more or less the air temperature 15.7 to 33.7 °C. The salinity ranged from 0.79 to 3.00 ppt. This means that the lakes are mixo-oligohaline. The depths ranged from 1.5 to 23 m while the secchi disc readings ranged from 0.8 to 2.2 m. The pH values lie always in the alkaline side and ranged from 8.8 to 9.1. The CO3 values fluctuated from 18.16 to 30.97 mg/L, while HCO3 varied from 130.18 to 182.51 mg/L. The lakes are characterized by high level of dissolved oxygen that ranged from 7.48 to 9.56 mg/L. The chemical oxygen Demand(COD) values varied from 1.7 5.3 mg/L. Magnesium concentrations (22.59 mg/L -616.8 mg/L) were much higher than calcium values (139.28 mg/L-341.67 mg/L). Organic nitrogen was much higher than other nitrogen forms and ranged from 0.77 mg/L to 2.05 mg/L. The orthophosphate concentrations ranged from 19 pg/L to 60.4 pg/L and organic phosphorus values fluctuated from 42.9 pg/L to 137 pp/L. Silicate-Si levels varied from 4.04 to 9.45 mg/L. The net primary productivity reached to its maximum value during Summer while its minimum was recorded in Winter. Its values varied from 120.81 to 221.4 mg C/m4/h.