We developed generalised additive mixed models (GAMMs) to infer spatiotemporal trends of environmental PCB concentrations from an extensive dataset (n = 1219) of PCB concentrations measured between 1991 and 2010 in sediments of the Belgian Coastal Zone (BCZ) and the Western Scheldt estuary. A GAMM with time, geographical zone, periodicity and the organic carbon - water partition coefficient as covariates explained 49% of the variability in the log transformed PCB sediment concentrations. The time trends unraveled two to threefold PCB concentration decreases in the BCZ during the last 20 years. However, in the Western Scheldt estuary, time trends were spatially heterogeneous and not significantly decreasing. These results demonstrate that international efforts to cut down emissions of PCBs have been effective to reduce concentrations in open water ecosystems like the BCZ but had little effect in the urbanised and industrialised area of the Scheldt estuary.