To find proper water quality management strategy for oxygen consumption organic matters in Jinhae bay, the physical process and net supply/decomposition in terms of COD was estimated by three-dimensional eco-hydrodynamic modeling. The estimation results of physical process in terms of COD showed that transportation of COD was dominant in loading area from land to sea, while accumulation of COD was dominant in $middle{sim}bottom$ level. In case of surface level, the net supply rate of COD was $0{sim}60;mg/m^2/day$. The net decomposition rate of COD was $0{sim}-0.05;mg/m^2/day$($-5{sim}-10$ m, in depth) to 2 level, and $-0.05{sim}-0.20;mg/m^2/day(10m{sim})$ to bottom level. These results indicate that the biological decomposition and physical accumulation of COD are occurred for the most part of Jinhae Bay bottom. The variation of net supply or net decomposition rate of COD as reducing land based input loading is also remarkable. Therefore, it is important to consider both allochthonous and autochthonous oxygen demanding organic matters to improve the water quality of Jinhae Bay.