Indicators related to organic matter are important when assessing aquatic environment quality. The chemical oxygen demand (COD) is widely used as a water quality reference. However, oxidizing agents used to determine the COD can oxidize refractory organic matter that is not pollutant and can persist in the ocean for thousands of years. This means the COD can misrepresent the water quality. The actual water quality can be indicated better by the biochemical oxygen demand (BOD) than the COD, but determining the BOD is time-consuming and gives variable results. In this study, the optical properties of dissolved organic matter in water samples from the Chinese coast that had been incubated for a long time or directly oxidized using COD oxidant were analyzed. The results indicated that the oxidizing agent rapidly oxidized 22.93% ± 4.96% of refractory dissolved organic matter (RDOM) that was resistant to microbial degradation, implying that RDOM made a marked contribution to the COD. Meanwhile, size-fractional fluorescence spectroscopy and COD measurements indicated that the COD of the >0.7 μm fraction and the fluorescence intensity of the protein-like component significantly positively correlated with the BOD of the bulk sample. This indicated that, for monitoring organic pollutants in coastal waters, the COD of the >0.7 μm fraction could be used as a proxy for the standard COD and that the fluorescence intensity of the protein-like component could be used as a convenient proxy for the BOD. The method can help retain recalcitrant organic matter in seawater to act as a carbon sink.