Sediment cores were collected from four outlets in the Pearl River Estuary (Guangdong Province, China) and dated using the 210Pb method to investigate the pollution history of the area due to its relatively stable sedimentation status and hydrographic conditions in recent decades. The ages of the sediment cores were dated over 40 years (1968–2015). The concentrations at the four outlets ranged from 2.21 to 48.52 ng g−1 dw for nonylphenol and were non-detectable for 23.64 ng g−1 dw for bisphenol A (BPA), which exhibited a decreasing trend from north to south as well as seaward. The fluxes (2.84 to 112.91 ng cm−2 yr−1 and non-detectable to 59.33 ng cm−2 yr−1 for nonylphenol and bisphenol A, respectively) stabilized in the 1980s to 1990s due to the construction of sewage treatment systems. The fluxes increased again in the 21st century, which reached a peak ca. 2010 but declined in recent years due to the establishment of regulations and the decreasing number of industrial enterprises. Fluctuations in the pollution composition coincided with industrial development and governmental policies.