In Egypt, the Water Quality of fresh waterways, especially those receiving the wastewater from agricultural drainage such as El-Salam Canal is every, now, and then, precarious for some water use. Although, Egypt relies on this marginal water quality in order to cover the resulting gap between water needs and supply. The reuse of drainage water appears to be one of the most promising, practical, and economical means of increasing the Egyptian water budget in which the Government of Egypt has been looking for. The use of mathematical models for the quality assessments of waterways can be considered as one of the effective and practical assessment tools. This paper simulates the self-purification controlling of the water quality of Bahr Hadus Drain (BHD) using QUAL2K water quality model. The three-step approach, on Bahr Hadus Drain, was simulated with proposed hydraulic structures (I.e., weirs) at certain locations. Three different weir types were investigated with fixed height at the proposed locations. Then the best weir type from the first step was selected for simulation of the second step at a specified location and, investigated for the impact of the weir height on the water quality. It is concluded that there is a correlation between water depth and weir height on water velocity and improvement of dissolved oxygen. In the third step, logarithmic regression models have been developed describing this relationship.