A numerical simulation was conducted on perfluorooctane sulfonate (PFOS) in the Gwangyang Bay using a multi-box model to estimate the transport of organic chemicals in the coastal environment. The results of the sensitivity analysis on dissolved PFOS and PFOS in Particulate Organic Carbon (POC) indicate that they were most significantly influenced by the adsorption rate, desorption rate, and sinking velocity coefficients. PFOS in phytoplankton was found to be sensitive to bio-concentration and the excretion rate. The results of the mass balance indicate that the standing stocks of PFOS in water, POC, and phytoplankton are 345.55 g, 63.76 g, and 0.11 g, respectively, in the inner part and 149.90 g, 27.51 g, and 0.05 g, respectively, in the outer part. Considering flux in the inner part, adsorption to POC had the highest value among transition paths. The next highest were desorption, outflow to the outer part, and inflow to the inner part. Outflow into the open sea was found to have the highest value for the outer part.