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Biogeochemical provinces are an important aid to identify homogeneous biogeochemical characteristics and underlying ecosystem dynamics in the open ocean. This macroscale approach, however, does not appear to be applicable to marginal seas for disregarding various small scale changes. Here, we adopted two observation schemes throughout the typical marginal seas, the South China Sea (SCS) and Straits of Malacca (MS), with continuous surface‐water sampling during March and May 2018. Spatial and seasonal heterogeneity of hydrological and dissolved organic matter (DOM) properties was investigated. With a novel combination of chromophoric DOM index and classical biogeochemical parameters (temperature, salinity, chlorophyll‐a, and bathymetry), we delineated five biogeochemical provinces in each season to integrate DOM pools and investigate region‐specific and season‐dependent biogeochemical processes. The results showed that the SCS basin was seasonally modulated by biological activities and photodegradation, resulting in the biologically active DOM pools. The western SCS seasonally received terrestrial DOM, subjected to the western boundary current under monsoon regulation. The MS was found to serve as an efficient carbon source of terrestrial substances, which exported to the northern Indian Ocean during the Northeast Monsoon. The delineation favored the simplification of complex biogeochemistry and allowed us to predict future trends in this dynamic system. Chromophoric DOM index was proven applicable to the delineation of marginal seas, that shed the light on the potential applications in biogeochemical provinces in dynamic systems. Plain Language Summary: The concept of biogeochemical provinces has been put forward to identify distinct environmental conditions and to better interpret complex biogeochemical processes. Such approaches, however, have rarely been applied to the marginal seas, which are an ever‐changing seascape and provide global focal points. Assessment of oceanic dissolved organic matter (DOM) dynamics was the key building block for understanding the biogeochemical cycle. In our study, we depicted seasonal DOM dynamics in response to environmental forcing in the surface of the South China Sea and the Straits of Malacca, and incorporated the chromophoric DOM (CDOM) index to propose a biogeochemical province delineation in the study area. Our results highlight that the refined scheme of biogeochemical province delineation effectively interprets the complex biogeochemistry in marginal seas by incorporating CDOM index. Key Points: The complexity of the South China Sea was emphasized with the spatially and seasonally heterogeneous dissolved organic matter (DOM) and biogeochemical forcingThe Straits of Malacca serve as an efficient source to export humic‐like terrestrial DOM to northern Indian Ocean during Northeast MonsoonThe refined biogeochemical province delineation scheme effectively interprets biogeochemistry in marginal seas by incorporating chromophoric DOM (CDOM) index [ABSTRACT FROM AUTHOR]