Abstract The sediment sources in the southern Okinawa trough (SOT) are still controversial and few studies have focused on the effects of transport processes on the elemental composition of initial terrigenous materials. Here we present rare earth element (REE) and trace element data on siliciclastic sediments from 14C age-dated Core S3, which was collected from the SOT, to provide reliable evidence for illustrating the modified effects of marine environments on terrigenous sediments deposited at different stages and exposing changes in sediment source over the past 3 ka. Compared with bulk sediments, the siliciclastic sediments in S3 have more variable REE fractionation parameters and lower middle REE (MREE) contents. Our REE data indicate that during river-sea processes, MREE-enriched fractions such as Fe–Mn oxides and carbonate were added to the original terrigenous sediments before deposition, weakening the degree of REE fractionation in the initial sediments; thus, care should be taken when using REE data from bulk samples to decipher source changes. The temporal changes in sediment source in S3 can be broadly identified based on the REE fractionation parameters of the residual fractions, and the results are largely consistent with the findings obtained by heavy mineral examinations. Units 1 and 3 are dominated by reworked shelf sediments of Changjiang origin,while the proportion of Taiwan-derived sediment is notably higher in Units 2 and 4. The sediment flux of Taiwan origin in the SOT was much smaller than previously thought. Huanghe-derived sediments and volcanic materials did not contribute significantly to the late Holocene sedimentation in the SOT. The large variations in sediment sources in S3 were possibly caused by changes in transport patterns driven by time-dependent changes in oceanic currents.