ABSTRACT:This research studies the impact of water level control structures on self-assimilative capacity of rivers and on fish habitat. Constructing a water level control structure in a river reach will alter its hydraulics as well as its water quality, thermal regime and fish habitat. A mathematical model is developed to simulate river hydraulics, water quality, temperature and fish habitat. Diurnal dissolved oxygen concentrations are investigated to show their impact on fish. A case of a Nile River reach was studied to investigate the impact of the existence of the Esna barrage on the water quality and fish in its upstream reach. The barrage has negative impacts on the upstream self-assimilative capacity of the rivers. The waste load that the river could absorb was only 54 % (at low flow) and 78 % (at high flow) of the entire load if no barrage was present. Including in the simulation of the effects of photosynthesis and respiration, the above mentioned percentages were raised to 54 % and 91 %, respectively. Although water level control structures have negative impacts on the upstream self-assimilative capacity of the rivers, they have positive effect on downstream dissolved oxygen concentrations due to reaeration that happens across them. Downstream dissolved oxygen concentration increased by 6 % from its upstream concentration value. The barrage has a positive effect on fish habitat in the upstream section. The weighted usable area of Tilapia fish is doubled in case of barrage existence. The barrage causes a slight decrease in water temperature that reaches an average of 0.13 degree in the month of June.