Polychlorinated biphenyls (PCBs) are toxic, persistent, and lipophilic chemical compounds that accumulate to high levels in harbor porpoises (Phocoena phocoena) and other cetaceans. It is important to monitor PCBs in wildlife, particularly in highly exposed populations to understand if concentrations are declining and how levels relate to toxicological thresholds and indices of health like infectious disease mortality. Here we show, using generalized additive models and tissue samples of 814 U.K.-stranded harbor porpoises collected between 1990 and 2017, that mean blubber PCB concentrations have fallen below the proposed thresholds for toxic effects. However, we found they are still associated with increased rates of infectious disease mortality such that an increase in PCB blubber concentrations of 1 mg kg–1 lipid corresponds with a 5% increase in risk of infectious disease mortality. Moreover, rates of decline and levels varied geographically, and the overall rate of decline is slow in comparison to other pollutants. We believe this is evidence of long-term preservation in the population and continued environmental contamination from diffuse sources. Our findings have serious implications for the management of PCB contamination in the U.K. and reinforce the need to prevent PCBs entering the marine environment to ensure that levels continue to decline.