Detrital apatite is a promising accessory mineral for reliable fingerprinting of the protolith composition of detrital sediment. Here, we present the geochemical compositions of detrital apatites from four sections of a high-resolution (~140 cm/kyr) sedimentary archive from the southern Okinawa Trough (SOT) for constraining sediment source rock types and establishing changes in provenance. A series of diagrams based on the geochemical data show that apatites in Section 1 derived mainly from mafic/intermediate rocks, while apatites in the three younger sections largely originated from mafic/intermediate rocks and acid rocks. Further, the four sections included a few contributions of apatites from alkaline rocks and metamorphic rocks. Through a comprehensive analysis of controlling factors and regional stratigraphy in the study area, we concluded that sediments in the SOT are the weathering/erosion products of sedimentary and meta-sedimentary rocks in the western and northeastern Taiwan Island, with ultimate sources containing a wide variety of rock types. The sediment from rivers in eastern Taiwan did not significantly contribute to deposition in the SOT. Apatites in Sections 2–4 showed strong geochemical similarity but differed from those in Section 1, indicating that the types of weathered/eroded sedimentary rocks in the weathering profile of river drainage basins of Taiwan Island changed in Section 2 (2010–1940 cal. yr BP) and have remained stable since then.

Frequent volcanic activity has occurred in the Okinawa Trough (OT) during the late Quaternary, which attracted much attention to the origin of volcanic rocks. Pumice collected from the seafloor has been extensively investigated, whereas few studies paid attention to the pumice in the sediment. The geochemical compositions of pumice preserved in sediments generally provide insight into past volcanic activity and regional magmatism. Here, we present major and trace element compositions and Sr-Nd-Pb isotope data, together with the established age framework for pumice samples recovered from sediment core S9 in the middle OT (MOT) to investigate their possible formation. Compositionally, the S9 pumice samples are dacite and are characterized by relatively higher Sr (⁸⁷Sr/⁸⁶Sr = 0.70480–0.70502) and Pb (²⁰⁶Pb/²⁰⁴Pb = 18.321-18.436, ²⁰⁷Pb/²⁰⁴Pb = 15.622–15.624, and ²⁰⁸Pb/²⁰⁴Pb = 38.52–38.63) and lower Nd (¹⁴³Nd/¹⁴⁴Nd = 0.51272–0.51274) isotope compositions than basalts from the MOT. The geochemical compositions of pumice clasts from different layers of core S9 display no temporal variation trends and vary within narrow ranges. On the basis of the geochemical characteristics of S9 pumice samples, we infer that the parent magma of these samples might generate from hybrid magma through an extensive fractional crystallization process. The Indian Ocean MORB-type mantle was first metasomatized by the subducted Philippine Sea sediments to form the primitive magma; then, followed by assimilation of a small amount of lower crustal component occurred in the lower crust. The long-term magmatism and relatively consistent isotopic compositions indicate that a magma chamber might have existed in the lower crust of the MOT between 11.22 and 12.96 cal. ka BP.