The main objective of this paper is to study the variation of some water quality variables along Rosetta Branch, to study the impact of drains discharging their wastes directly on the water quality of the branch and to define the optimum scenario requires overcoming the serious problem of the pollution in the branch. Water samples were collected from the branch as well as from the outfall of the drains during January 2011, August 2011, January 2016, August 2016, and March 2017 and analyzed for physicochemical parameters according the standard procedures. The Results indicated that, there is a degradation in water quality along the area located downstream El-Rahawy drain. This was reflected by low dissolved oxygen concentration that reaches to 0.07 mg/l. As well as, the BOD value was also recorded high values of 110 mg/l. These values were found 18 times higher than the allowable limits of law 48/year 1982 and its ministerial decree. It is worth to mention that, the area along Rosetta Branch comply with the permissible limits of the value of NH3 recommended by law 48 year 1982, except the area located downstream El-Rahawy and Sabal drains. Different scenarios are applied using Duflow model. The study concluded that, the water quality along Rosetta Branch has been significantly impacted with the drains especially El-Rahawy and Sabal, which consider the worst drains. The best scenario is the treatment of El-Rahawy drain with biological biofilm activated with aerator that improves the water quality along Rosetta Branch based on applying Duflow model.