Atmospheric reaeration process plays a key role in degradation of organic matter and self-purification processes affecting dissolved oxygen (DO) concentrations in rivers and streams. Moreover, water quality (WQ) processes can be highly dependent on flow velocity conditions. Where, highly reaeration rates are positively correlated with high flow velocity. Therefore, the present work reports deep insights on the role of flow velocity with reaeration process in the concentration of DO and biochemical oxygen demand (BOD5). This study was applied along the largest agricultural drainage water reuse project, El-Salam Canal in Egypt. The hydrodynamic (HD) characteristics and WQ parameters (DO and BOD5) along the canal were simulated using a one-dimensional HD and WQ model (MIKE 11). The simulated results indicated that the canal was deteriorated towards El-Salam Canal after mixing with El-Serw and Bahr Hadous drains. Statistical regression fitted line and Pearson correlation analysis, were performed on the simulation results of the reaeration rates with flow velocity and WQ values, indicating a significant correlation. Accordingly, water velocity should be taken into account as a key factor for describing the WQ change.