The ecosystem model was applied to estimate the regional distribution of the net production(or consumption) of phytoplankton and the net uptake(or regeneration) rate of nutrients in Masan Bay for scenario analysis to find a proper management plan. At the surface level, net production of phytoplankton is 200 mgC/㎡/day at the entrance of the bay, and 400∼1000 mgC/㎡/day at the center of the bay. The inner area of the bay showed more than 2000 mgC/㎡/day. All areas of the bottom level have a net consumption, with the center of the bottom level showing more than 600 mgC/㎡/day. For dissolved inorganic nitrogen, the results showed a net uptake rate of 100∼900 mg/㎡/day at the surface level. It showed that the net regeneration is above 50 mg/㎡/day at the bottom level. For dissolved inorganic phosphorus, the net uptake rate showed 10.0∼80.0 mg/㎡/day at the surface level, and the regeneration rate showed 0∼20.5 mg/㎡/day at the bottom level. Therefore, in order to control the water quality in Masan Bay, it is important to consider the re-supplement of nutrients regenerated in the water column.