Tropical marginal seas host unique sedimentary archives that may be exploited to reveal past changes in continental erosion, chemical weathering, and ocean dynamics. However, these records can be challenging to interpret due to the complex interactions between climate and particulate transport across ocean margins. For the southern South China Sea over the last 90 thousand years, we observe a contrasting temporal relationship between the deposition of clay minerals (smectite) and magnetic minerals (hematite), which were associated with two different hydrodynamic modes. Fine-grained clay minerals can be carried in suspension by ocean currents, leading to a rapid response to regional climate-driven inputs. In contrast, changes in magnetic mineralogy were closely associated with bedload transport and resuspension linked to glacial-interglacial sea-level variability. Overall, this study indicates that the transfer pathways and mechanisms imparted by varying hydrodynamic conditions exert a substantial influence on the distribution of terrigenous material in continental shelf sediments.