To establish a comprehensive management strategy, as part of the optimization of cultural practice for an oyster rack culture system, we used a numerical model to estimate the primary production in the waters on the eastern coast of Wando island, South Korea. The estimated primary production ranged from 17.12 to 1052.55 mgC m −2 day −1 (204.22 ± 224.75 mgC m −2 day −1 in average). Except for the times of peak phytoplankton blooms, the estimated primary production (PP) was consistently under 200 mgC m −2 day −1 , which is more similar to the value of PP measured off the western coast of South Korea than the southern coast. No clear relationship was observed between nitrogen content and rainfall with the exception of heavy rainfall events, indicating that precipitation might not be the main source of nutrients in these waters. No clear influence was observed from Doam tidal discharge, located 24 km north from these waters due to main tide comes in this area from the channel between Gunwe-myeon in Wando island and Pukpyeong-myeon in Haenam-gun. Because of the shallow water depth and strong tidal current, resuspension of sediments, which causes an input of nitrogen into the system, could be easily caused by even mild wind and the infrequent passing of ships. Microscopic examination of the phytoplankton composition showed additional contribution of benthic species such as Paralia sulcata into the waters, which increase the productivity of oyster farms in the waters. The availability of nitrate and phosphate for primary production was temporarily limited throughout most of the spring and autumn blooming season.