Bisphenol (BP) analogues are widely used as industrial materials and various product additives and are inevitably released into environment. However, knowledge on the sources of different BPs, especially those from urban rainfall runoff to the receiving rivers is very limited. In this study, 15 BPs were determined in surface water, sediments, wastewater treatment plant (WWTP) and rainfall runoff samples in the Pearl River region, South China. Eleven BPs were detected in surface water and sediments of the Pearl Rivers. BPA was the dominant compound up to 2080 ng/L in surface and 1970 ng/g in sediments, followed by BPF, BPS, BPTMC and BPAF. In WWTPs, 10, 9 and 8 BPs were detected in influents, effluents and excess sludges, respectively, with total BPs (ΣBPs) concentrations in effluents still at thousands ng/L, suggesting incompletely removal of BPs. Five BPs were detected in urban rainfall runoff samples, with the ΣBPs concentrations up to 7740 ng/L. Mass loads of ΣBPs from the rainfall runoff (5800 kg/y) were almost equivalent to the source from WWTPs (7370 kg/y) in the region, implying that the urban rainfall runoff was a potential source for BPs into the receiving river. The calculated estrogenic activity contributed by BPs showed low to median risks in sources and receiving rivers. But BPs are always as mixtures with other potential endocrine disrupting chemicals (EDCs) which probably pose high estrogenic activity risks. Hence, effective measures should be taken to decrease the input of EDCs from sources to receiving rivers. Display omitted •15 Bisphenol (BP) analogues in river, WWTPs and rainfall runoff were investigated.•BPA was the dominant, followed by BPF, BPS, BPTMC and BPAF in most inputs.•The mean ΣBPs in street and courtyard runoff were 2410 and 232 ng/L, respectively.•The mass load of BPs from rainfall runoff was almost equal to WWTP effluents.•BPs posed low to median estrogenic risks in the Pearl River Delta region. This study showed the wide detections of bisphenol analogues from different sources to the Pearl River system, and emphasizes the importance of considering urban rainfall runoff as a potential source of bisphenols for the receiving rivers.