Water intakes are designed to carry water supply pipes to reach channel water specifically during periods of minimum water stages. If the water levels fall below expectations, it will cause some of intakes out of service and negative impacts on the intakes. In this paper, the effects of flow reduction ratio values on the intakes along the River Nile from Esna Barrage to Naga Hammadi Barrage are studied numerically. Different scenarios were considered for this reduction and mathematical model (SOBEK-1D) was used to compute water level along River Nile. The results showed that the reduction in water levels produces negative impacts on the intakes and illustrated to assist the decision maker to solve the problems of affected intakes. These reductions are maximum with 8.9% at Naga Hammadi Barrage for the last scenario and minimum with 0.2% for the first scenario, the reduction in water levels decreases Nile water velocities and reduction water level up to 5% produces small influence on the safe navigation. The scenario of only 5% reduction the not working intakes will be more than 59%.