Lake Manzala is the largest lake along the Egyptian Mediterranean coast. It is in northeastern Egypt on the Nile delta near Port-Said City. The lake is long, quite shallow and suffering from severe ecological problems during the last years. The discharge of polluted water from five main drains is drained in the lake causing negative ecological, health, social and economic impacts. The main goal of this paper is to investigate the effects of excessive drainage water on both water levels and salinityin the lake. A 3-D hydrodynamic numerical model was developed for the lake using Delft 3D modelling system. Mitigation process has been studied to enhance the mixing between lake water and seawater. The optimum mitigation was achieved by reducing the water level in the lake through decreasing the effluents from Bahr El-Baqrdrain and enhancing the density current from seawater to the lake via increasing water depth inside the lake by dredging the total area of the lake. Also, all obstacles due to human interaction such as fish cages, weeds, and islands inside the lake must be removed.