We analyzed three decades of field observations in the North Sea with additive models to infer spatiotemporal trends of chlorophyll a concentration, sediment organic carbon content, and polychlorinated biphenyls (PCBs) concentrations in mussels and sediments. By doing so, we separated long-term changes in PCB concentrations from seasonal variability. Using the inferred seasonal variability, we demonstrated that phytoplankton blooms in spring and autumn correspond to the annual maxima of the organic carbon content (r = 0.56; p = 0.004) and the PCB concentrations in sediments (r = 0.57; p = 0.004). Furthermore, we found a negative correlation between the PCB concentrations in sediments and in blue mussels (Mytilus edulis; r = -0.33, p = 0.012), which is probably related to the cleansing of the dissolved PCB phase driven by sinking organic matter during phytoplankton blooms and the filter-feeding behavior of the blue mussel. The present research demonstrates the role of seasonal phytoplankton dynamics in the environmental fate of PCBs at large spatiotemporal scales.