Bandon Bay (Surat Thani Province) is one of the most productive coastal areas in southern Thailand. The Tapi River and 18 channels are the main sources of freshwater, nutrients, organic matter and sediment to the bay and the loading of freshwater and nutrients provide essential support for the production of phytoplankton in the estuarine ecosystem. Bandon Bay is important as natural spawning, nursery and feeding grounds for shellfish such as oysters, blood cockles, green mussels, short-necked clams, mud crabs and shrimps, and the estuary also serves as an excellent area for mariculturing of shellfish. In fact, oysters and blood cockles cultured in Bandon Bay are now being exported worldwide. However, Bandon Bay is also a textbook example of overexploitation of coastal resources in the tropics including all the derived changes in the estuarial ecosystem with severe socio-economic consequences. Hence, there is an urgent need for setting up an integrated management plan for a sustainable use of shellfish resources in Bandon Bay. The present study attempts to integrate water quality simulation results, socio-economic data and information on existing shellfish resource use in the process of proposing a set of sustainable management strategies for shellfish resources in Bandon Bay. These strategies involve: (1) using water quality modeling to monitor ecological and environmental changes in shellfish culture beds and their natural habitats in the process of setting up a master plan for management of waste water discharge into Bandon Bay; (2) zoning of shellfish mariculture in the coastal area in order to solve conflicts between resource users; (3) setting up a clear system for taxation of mariculture where the revenue may be used for (4) setting up and managing mangrove strips as filters of pollution and sediment around Bandon Bay; and finally (5) it is suggested to form a committee with members representing all relevant stakeholders plus the local government in order to work on resolving the existing and potential future conflicts over resource usage in Bandon Bay. This methodology may be seen as an important contribution towards a Bandon Bay sustainable management approach, based on the principles of integrated coastal zone management because it is science-based and takes into consideration the needs and perceptions of people involved in coastal resource extraction.