Coastal waters in South Johore, Malaysia are polluted to various degrees. The major pollution sources are domestric wastes from human settlements, agro-based wastes from palm oil mills and rubber processing factories, industrial effluents from industrial estates and discharges from animal farms. These pollution problems have adversely affected resources such as fisheries, recreational potential as well as the general aesthetic quality of the coastal environment particularly the Inner Johore Strait. Hence proper management and control measures are urgently needed to protect and further enhance the water quality to ensure environmentally sustainable development. This study examines various management options to control the pollution in the Inner Johore Strait. The options involve partial opening as well as complete removal of the Causeway to improve the tidal flow for more effective dilution and dispersion of pollutants. Computer simulation models are used to assess the impacts of the proposed options.