Globally, coastal aquaculture is growing due to the large demand for marine products. Specific impacts caused by coastal aquaculture on the environment include the discharge of culture farm effluents, stress on ground water (the absence of recycling), nutrient pollution, and diseases of cultured animals. Three methods, integrated multitrophic aquaculture (IMTA), recirculating aquaculture system (RAS), and beneficial bacteria for aquaculture, have been developed to solve these problems. In this study, the advantages of IMTA and RAS were integrated to develop a novel multitrophic recirculating aquaculture system (MRAS) to adapt to the farm-scale culturing of milkfish (Chanos chanos). The photosynthetic bacteria Rhodovulum sulfidophilum was added to enhance the performance of the farm-scale milkfish MRAS. This setting could promote growth of beneficial bacteria, such as the nitrogen cycle-associated microbial community and the anoxygenic phototrophic Acidobacteria community. The ammonia level was reduced, and the total phosphorous level was stable in the water recycled in the MRAS. The cyanobacteria, algae, Vibrio, Escherichia, and other potential pathogenic bacteria communities were inhibited in the MRAS. This study provides an effective design of a water recycling aquaculture system. Milkfish, Asian tiger shrimp (Penaeus monodon), Asian hard clam (Meretrix lusoria), and seaweed (Gracilaria sp.) can be cultured and simultaneously produced in the system.