Three dated sedimentary cores were collected for the investigation of temporal trends and the environmental loadings of nonylphenol (NP) and bisphenol A (BPA) in recent decades in the Pearl River Estuary (PRE), South China and the adjacent South China Sea (SCS). The peak fluxes of NP and BPA occurred in the mid-1980s in the PRE, coincident with the rapid economic growth in China. The decline of NP and BPA fluxes is attributable to the implementation of sewage treatment in the late 1980s in the Pearl River Delta (PRD). Multi-model distributions were observed for the fluxes of NP and BPA in the SCS with the peak fluxes occurring in the late 1950s and the mid-1970s respectively. The fluxes of NP and BPA have increased since the 1990s due to the lack of adequate wastewater treatment facilities and the constant economic growth. Nonylphenol was quantifiably detected in sediments predating its widespread application (1940s), suggesting the downward penetration of NP in the sediment columns. The characterization results revealed that NP and BPA were preserved well and the isomer-selective degradation of NP did not occur significantly in the sediment cores. The environmental loadings of NP and BPA in the PRE sediments were roughly estimated to be 124 t and 1.7 t respectively over the past 30 years.