Coastal aquaculture is a traditional practice in Southeast Asia. Accelerated development in the last three decades has created negative environmental impacts, such as extensive mangrove conversion to ponds, changes in hydrologic regimes in enclosed waters due to proliferation of aquaculture structures, and discharge of high levels of organic matter into coastal waters. Similarly, the increasing deterioration of coastal water quality resulting from the discharge of domestic, agricultural and industrial wastes into coastal waters has affected aquaculture production and profitability. Furthermore, the increased frequency of red tides in the region has posed serious threats to coastal aquaculture, especially to mollusc cultivation. The introduction of management measures to mitigate deteriorating coastal water quality and the adverse environmental impacts of aquaculture development has now become a matter of urgency to the region.