Current mass balances of C, N, and P were estimated using a model (Fluxin = Fluxout + ΔFlux) from Gamak Bay, Korea, in August 2017, where eutrophication and reducing conditions are prevalent. To examine the current fluxes of particulate organic carbon (POC), nitrogen (PON), and phosphorus (POP), sinking and re-floating sediment traps were deployed, a sediment oxygen demand (SOD) chamber experiment and ex-situ nutrient incubation experiment were conducted, and Fick’s first law of diffusion was applied. The principal component analysis and cluster analysis were performed to identify the three groups of water masses based on the characteristics of the bay, including the effects of the reducing environment due to the anoxic water mass using 14 bottom water quality parameters. In the reducing environment (sampling point GA4), the SOD20 flux was 3047.2 mg O2/m2/d. Additionally, the net sinking POC flux was 861.0 mg C/m2/d, while 131.8% of the net sinking POC flux (1134.5 mg C/m2/d) was removed toward the overlying water. This indicates that the organic matter that had been deposited was decomposed as a flux of 273.6 mg C/m2/d. The net sinking PON flux was 187.9 mg N/m2/d, whereas 15.8% of the net sinking PON flux was eluted, and 84.2% remained in the surface sediments. The dissolved inorganic nitrogen (DIN) elution flux from the surface sediments consisted of NH4+ elution (33.7 mg N/m2/d) and NOx− elution (−4.1 mg N/m2/d) fluxes. Despite the net sinking POP flux being 26.0 mg P/m2/d, the 47.7 mg P/m2/d of DIP elution flux (179.5% of the net sinking POP flux) was eluted to the overlying water. Similar to C mass balance, the additional elution flux occurred. Therefore, severe eutrophication (16.5 of the Okaichi eutrophication index) with the lowest N:P ratio (2.6) in GA4 was noted. This indicates that not only the freshly exported organic matter to the surface sediments but also the biochemical processes under anoxic conditions played an essential role as a remarkable nutrient source–particularly P–for eutrophication in Gamak Bay, Korea.