A major re-organization of regional drainages in eastern Tibet and south-western China took place in the Cenozoic as deformation from the growing Himalayas and Tibetan Plateau affected an increasingly wider area. The effects of these changes on the regional sediment routing systems is not well constrained. This study examines the geochemical and Nd signatures of sedimentary rocks from the Ying-Qiong and Nanxiong basins on the northern margin of the South China Sea to constrain and identify any significant changes in sediment source. Upper Cretaceous to Lower Eocene sedimentary rocks in the Nanxiong Basin show higher Th/Sc, La/Sc, Th/Cr and Th/Co ratios and lower Eu/Eu* ratios than PAAS (post-Archaean Australian Shale), which indicates that Palaeozoic sedimentary rocks of the South China Block were the main basin sediment source. In contrast, Oligocene to Pleistocene sedimentary rocks of the Ying-Qiong Basin show an abrupt change in these trace-element ratios between 16·3 and 10·4 Ma, indicating a mid-Miocene shift in provenance. ɛNd values from the Ying-Qiong Basin (range = −11·1 to −2·1) reinforce this, with pre-13·8 Ma sedimentary rocks having average ɛNd of −5·6 (range = −2·1 to −7·4), and post-13·8 Ma sedimentary rocks having average ɛNd of −9·3 (range = −8·7 to −11·1). During the Oligocene, the centre of rifting transferred south and basins on the north margin of the South China Sea experienced rapid subsidence. Further uplift and erosion then exposed Mesozoic and Cenozoic granites that supplied large amounts of granitic detritus, especially to the Ying-Qiong Basin. Then a change occurred at ca 13 Ma resulting in less input from local sources (i.e. the fault blocks formed by Mesozoic-Cenozoic tectonics and magmatism) to an increasing contribution of older continental material, mostly from Indochina to the west of the South China Sea.