In terms of downward transport, suspended particulate matter (SPM) from marine or terrigenous sources is an essential contributor to the carbon cycle. Within mesoscale environments such as seagrass ecosystems, SPM flux is an essential part of the total carbon budget that is transported within the ecosystem. By assessing the total SPM transport from water column to sediment, potential carbon burial can be estimated. However, SPM may decompose or reforming aggregate during transport, so estimating the vertical flux without knowing the decomposition rate will lead to over- or underestimation of the total carbon budget. Here this paper presents the potential decomposition rate of the SPM in seagrass ecosystems in an attempt to elucidate the carbon dynamics of SPM. SPM was collected from the seagrass ecosystems located at Sikka and Sorong in Indonesia. In situ experiments using SPM traps were conducted to assess the vertical downward flux and decomposition rate of SPM. The isotopic profile of SPM was measured together with organic carbon and total nitrogen content. The results show that SPM was transported to the bottom of the seagrass ecosystem at a rate of up to (129.45±53.79) mg/(m²·h) (according to carbon). Considering the whole period of inundation of seagrass meadows, SPM downward flux reached a maximum of 3 096 mg/(m²·d) (according to carbon). The decomposition rate was estimated at from 5.9 µg/(mg·d) (according to carbon) to 26.6 µg/(mg·d) (according to carbon). Considering the total downward flux of SPM in the study site, the maximum decomposed SPM was estimated 39.9 mg/(m²·d) (according to carbon) and 82.6 mg/(m²·d) (according to carbon) for study site at Sorong and Sikka, respectively. The decomposed SPM can be 0.6%–2.7% of the total SPM flux, indicating that it is a small proportion of the total flux. The seagrass ecosystems of Sorong and Sikka SPM show an autochthonous tendency with the primary composition of marine-end materials.