“Blue carbon”, captured and sequestrated by marine organisms, has attracted attention as one of the major sink of the carbon emitted by anthropogenic activity. Shallow coastal ecosystems such as seagrass meadows and intertidal flats are recently proposed to be particularly important ecosystems for blue carbon. Blue carbon is sequestrated in aquatic systems as organic matter produced by photosynthesis and catabolism. Various organic matter compositions, having allochthonous and autochthonous origins, are mixed in shallow waters. The carbon sequestration time would be variable because each composition has different inflow/outflow and production/consumption rate. However, the origin and composition of organic matter are yet unknown in shallow coastal ecosystems. In this study, we evaluated the dynamics of organic matter, particulate organic matter (POM) and dissolved organic matter (DOM), in a subarctic brackish lagoon, where several sources of organic matter are potentially present. We used the mixing model using elemental and isotopic signatures to estimate the relative contribution of four sources (terrestrial, coastal, lagoon, and phytobenthos POMs) to the total POM. Terrestrial POM dominated at the river mouth but autochthonous POM (phytoplankton) was the most contributing source to the whole lagoon. The burial of these compositions of POM would be important as carbon sequestration processes. The optical and elemental techniques qualitatively indicated that the primary producers released DOM into the water column. Since the refractory fraction of DOM would be sequestrated from air CO2 for years to millennia, DOM released from shallow coastal ecosystems should be included as carbon sequestration process in addition to sedimented organic matter. Moreover, nutrients appeared to limit the primary production, indicating that nutrient dynamics is closely linked to carbon sequestration. Our comprehensive biogeochemical study demonstrates the linkage between the carbon sequestration processes and the environmental factors in shallow coastal ecosystems.