The culture of fish in cages has been shown to be economically efficiency; however, it produces large amounts of fish feces and uneaten food. These organic waste materials, containing significant levels of carbon, nitrogen, phosphorus, etc., can cause environmental damage and may result in decreased dissolved oxygen levels within cages, negatively affecting fish production. During an exploration of benthic taxa beneath cage culture, numerous nereids were recorded, including , an important seashore species of polychaete, feeding in the sediments. In the present study, a system of fish cage culture and were combined in a 40-day laboratory experiment to investigate the carbon/nitrogen budget and its effect on environmental optimization. The experimental design involved four treatments at the same fish density within the cage (Japanese flounder, , about 21 g/ind, 5 ind/cage) and different densities of (0, 50, 70 and 90 g; designated C, S1, S2 and S3). There were three replicates for each treatment. The cage was 60 cm in diameter by 30 cm deep. The fish and were starved for 24 h before being weighed. Five Japanese flounders and 20 g of were in the initial sample. All specimens were fed twice a day with artificial pellets at 07:30 and 18:00 during the experimental period. The amount of food was similar in each group and was adjusted according to the uneaten food in the control group. Uneaten food and fish feces were left in the system. The system had a steady flow rate of 250–300 L/day and light aeration was provided continuously. A simulated natural photoperiod (14:10, light/dark) was used throughout the experiments. At the end of the experiment, all animals were sampled, weighed after 24 h starvation, and oven-dried at 70 for 48 h for analysis. The results showed that the levels of carbon and nitrogen in the sediment were higher in the control (C) than in other treatments. There was no significant difference among treatments in the amount of carbon lost in respiration, or for the net output of organic carbon and nitrogen in water (> 0.05). The input of carbon and nitrogen was principally from food. In addition, there was no significant difference among treatments of the proportion of nitrogen for net output in water (> 0.05). The proportion of nitrogen output from the system was highest in the control, but there was no significant difference between C, S1 and S2 (> 0.05). The proportion of nitrogen accumulated in sediment was higher in the control than in either S2 or S3 (0.05). The proportion of carbon accumulated in sediment was highest in the control (0.05). The proportion of organic carbon for net output in water was higher in C and S1 than in S3 (0.05). The proportion of carbon output for the system was significantly lower in S3 than in S1 or the control (0.05). Both the carbon and nitrogen output ratios were lowest in the control. In the present experiment, was shown to be a significant consumer of uneaten food and feces in our model of “Japanese flounder cage culture and ”. Our novel model could be valuable in reducing carbon and nitrogen accumulation in the sediment beneath Japanese flounder cage culture and thereby improving the environment and enhancing fish production.