Geochemical data from South China Sea sedimentary rocks show the effects of both source composition and depositional environments. This enables us to link tectonic trends with erosion in the Pearl River region since c. 32 Ma. In particular, a shift in the geochemistry appears to signal a response to a well-recorded regional tectonic event at c. 23–25 Ma, probably corresponding to a jump in the seafloor spreading axis from the west to the SW within the South China Sea. This may correlate with the uplift of the West Yunnan Plateau and possibly also the eastern Tibetan Plateau. Clay mineralogy, sand–mud ratio, and major and rare earth element concentrations, also varied in response to the environment in the drainage areas of the palaeo-Pearl River. By comparing data from the modern sources and the sedimentary record from the northern South China Sea, especially the erosion–transportation–deposition patterns, three groups of index minerals (Ati, GZi, ZTR), as well as rare earth elements can be recognized. These are used to characterize the Pearl River from the east to the west, representing three different parent rock sources. The evolution of the palaeo-Pearl River can be tracked by variations of heavy minerals and key elements that are indicative of provenance.