The present paper aims to manage water and salt balance of Wadi El-Rayan Depression, El-Fayoum, Egypt. Data measurements from the study area were collected and analyzed. SOBEK-1D2D was employed and different scenarios were tested. The results of the study indicated that scenario 4 is the best for the current condition to manage Wadi El-Rayan Lakes in a better way. Also scenario 5 is the most suitable for the future condition. In conclusion, the management problem of water and salt balance is solved. A number of management steps are recommended to help the decision makers to set a management plan for Wadi El-Rayan Lakes.