With anthropogenic activities, the persistent organic pollutants (POPs) accumulated in estuary has been notably concern but the influences of complex hydrodynamic conditions on the fate of POPs in estuary have not fully understood. In this study, the bottom velocity and the concentration of suspended sediment in the Yangtze River Estuary (YRE) were determined using the Acoustic Doppler Current Profiler (ADCP), while the concentration of three typical POPs with distinguishing properties, including polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and organichlorine pesticides (OCPs), were determined simultaneously. Then three nonlinear equations were determined for identifying the hotspots of PCBs, OCPs and PAHs in the YRE. The results indicated the goodness-of-fitting of these three equations were satisfactory, indicating the bottom velocity and the suspended sediment level could be used as the reference factor of POPs. For the YRE, the north branch, the upstream of the north branch, and the mouth of the YRE are identified as the hotspots of PCBs, PAHs and OCPs, especially in the normal, flood and dry season, respectively. Simple structure and easy data availability make the results and methods presented in this paper to be easily used as a reference for POPs studies in other regions.