Lake Manzala, the largest of the northern Delta lakes of Egypt, has a great economic importance as a major natural resource of fish and salt. Unfortunately, the lake is suffering from the high inputs of pollutants from industrial, domestic, and agricultural sources. The present study aims to develop the proposed water quality management scenarios to assess and control lake pollution, the pollution sources as well as the pollution spread from the lake to the connected Mediterranean Sea. To apply study methodology, the work tasks divided into two main parts, the first part involved in modelling the lake environments by using Delft3D-WAQ hydrodynamic and water quality model to study the current status and predict the dynamic state of the Lake. This model was calibrated and validated by using various water quality datasets to simulate different scenarios. In the second part, the required lake water quality improvement scenarios were developed to solve the lake water quality problems. The study results showed that the first three developed scenarios that focusing on treatment drain effluent using primary, secondary treatment and surface wetland techniques respectively have a limited efficiency on lake water quality improvement. While the fourth scenario that involved on using biological biofilm techniques can improve lake water quality parameters. Moreover, the fifth scenario that proposed adding a new artificial inlet has a limitation due to the noted increases in lake salinity levels. The sixth scenario that proposed a diversion of some drains can improve lake water quality parameters but it can lead to a decrease in Lake water level. From water quality view point, the last scenario that applying a combination biological biofilm activated technique and also adding a new artificial inlet at northern lake region can represent the optimum scenario. Hopefully, this research will preserve the lake environment and contribute to the benefit of the man health as well. This approach could be extended to the hydrodynamic studies in similar large, shallow lakes anywhere in the world.