The objective of this research is to apply more scientific, quantitative methods and procedures of environmental investigation to the development of the natural environment and the improvement of the human environment during the establishment of a sewage treatment plant and special facilities using environmental accounting. This research was performed to develop a method of strategic environmental assessment on the operation of sewage treatment plant and reuse of shellfish seeding areas through the use of environmental accounting based on EMERGY evaluation. The result was applied to marine environment policy in order to evaluate the real wealth of the regional environment and economy for both the present phase and the proposed developed phase. Using results from the comparison of EMERGY indices between the present situation and future scenarios, cost benefit analysis was performed for three different scenarios: (I) construction of a new sewage treatment plant, (2) relocation and recovery of the shellfish seeding area, and (3) relocation and re-seeding of shellfish area and construction of a new sewage treatment plant. Cost-benefit ratios of the three scenarios are 1.88, 0.94, and 1.38, respectively.