This paper presents the preliminary results of the application of the ocean model (FVCOM) to replicate the hydrodynamic flows experienced within Lake El-Manzala, Egypt. The construction of this model is used to characterize the ecosystem of this shallow brackish lake and assess a range of sustainable water management strategies. Lake El-Manzala is the largest of the Egyptian shallow coastal lakes on the fringe of the Mediterranean Sea. The lake currently supports 30% of the fresh water fish farm production of Egypt. In recent years the aquatic health of the lake has significantly deteriorated due to an increase in the contamination of the lake by polluted inflows and over intensive aquaculture. The focus of this study is to develop a model that may be employed to investigate the causes, effects and potential solutions to the pollutant loads imposed on the lake. The model has been used to study the hydrodynamic effect that a 40% reduction in the polluted drain water inflows to the lake due to a diversion of this water towards the Sinai for land development. This study concluded that in the western zone of the lake this action slightly changed the magnitude and direction of the water flows and an increase in the salinity levels. Several other lake management scenarios were proposed and the environmental effects on the lake water quality are under investigation. It is concluded that the hydrodynamic models developed may be used to study the cause and effects of other aquatic pollution problems and permit the investigation of potential engineering solutions to improve water quality management.