Water intakes are structures that are designed to carry water supply pipes to reach channel water specifically during periods of minimum water stages such that it can ensure permanent water abstraction and supply. If the water levels fall below expectations, it will cause some of intakes out of service and negative impacts on the intakes. So it is important to study the impacts of flow reduction on the intakes along the River Nile from Esna Barrage to Naga Hammadi Barrage. Different six scenarios were considered for this reduction and mathematical models were used to compute water level along River Nile to study the impact on the intakes along the Nile River. Study results were highlighted and illustrated to assist the decision maker to solve the problems of affected intakes.