Chemical contamination by persistent organic pollutants (POPs) is one of the anthropogenic stressors for the deep sea. Here we use a coupled multi-compartment chemistry-transport model to simulate long-term transports and fate of polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT). We show that the pollution signal received by the surface waters through atmospheric deposition is propagating downward and that ocean currents can act as a secondary source of POPs. Besides considerable time lags with respect to the year of peak emission, we find in some areas, e.g., in the western and eastern North Atlantic temporal bimodal exposure toward the pollutants of mid-level and deep waters (200–1500 m). This is caused by vertical and horizontal transport through advection diffusion and particle sinking. We suggest that the combination of the same processes will lead to a re-rise of exposure in other sea regions in the future, including where deep-sea fisheries take place.