Field observations of persistent organic pollutants (POPs) in shelf seas presented abnormal phenomena such as high-concentration patches in offshore areas and different vertical profiles of POPs at the same location. We assumed that these phenomena were associated with the presence of bottom cold water mass (BCWM) in shelf seas and used a hydrodynamic-ecosystem-POP coupled model to confirm this hypothesis. Based on model results, with the formation of BCWM during summer, POPs accumulated inside BCWM due to their transport across the thermocline by the sorption to sinking particles. With the intensification of vertical mixing during winter, the release of POPs from BCWM induced high-concentration patches of POPs on the surface layer. Meanwhile, the low water temperature in winter was favorable for the gas deposition of POPs, which led to high surface concentrations of POPs. Because the accumulation of POPs in BCWM depended on the sorption of dissolved POPs by particles, not all types of POPs accumulated in BCWM. Some POPs even accumulated at the sea surface above the BCWM due to large gaseous deposition and weak sorption by particles. Using this feature, we proposed a prediction function for the accumulation of POPs in BCWM.