Persistent organic pollutants (POPs), including polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs) and hexachlorobenzene (HCB), bioaccumulate in marine ecosystems. Top predators contain high levels of POPs in their lipid-rich tissues, which may result in adverse effects on their reproductive, immune and endocrine functions. Harbour porpoises (Phocoena phocoena) are among the smallest of cetaceans and live under high metabolic demand, making them particularly vulnerable to environmental pressures. Using samples from individuals of all maturity classes and sexes stranded along the southern North Sea (n = 121), we show the generational transfer of PCBs, PBDEs and HCB from adults to foetuses. Porpoise placentas contained 1.3–8.2 mg/kg lipid weight (lw) Sum-17PCB, 9 mg/kg lw). This was particularly true for adult males (92.3% >9 mg/kg lw), while adult females had relatively low PCB levels (10.5% >9 mg/kg lw) due to offloading. Nutritional stress led to higher offloading in the milk, causing a greater potential for toxicity in calves of nutritionally stressed females. No correlation between PCB concentration and parasite infestation was detected, although the probability of a porpoise dying due to infectious disease or debilitation increased with increasing PCB concentrations. Despite current regulations to reduce pollution, these results provide further evidence of potential health effects of POPs on harbour porpoises of the southern North Sea, which may consequently increase their susceptibility to other pressures.