Near-total darkness and water depths below 200 m define the deep sea, Earth’s largest yet most poorly studied ecosystem. Sowerby’s beaked whales (Mesoplodon bidens), elusive deep-sea foragers, offer a unique opportunity to assess the impacts of anthropogenic pollutants in this remote environment. This study examined a range of legacy and emerging hydrophobic pollutants, including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), hexabromocyclododecane (HBCD), and polychlorinated alkanes (PCAs), across tissues from five stranded whales foraging in Swedish waters. Despite global efforts to reduce pollution, significant pollutant levels in these whales underscore the persistence of legacy contaminants and the widespread use of PCAs. Most pollutants were concentrated in lipid-rich blubber, while PCAs exhibited particularly high levels in whole blood (941-13100 ng/g lipid), indicating tissue-specific accumulation. Blubber pollutant levels were similar to those of harbor porpoises from the same waters, with p,p′-DDE (1020-2280 ng/g lipid) and PCBs (1230-1930 ng/g lipid) exceeding or nearing effect thresholds. Blood concentrations of legacy pollutants were approximately an order of magnitude higher than those in humans from the region, while PCA levels were comparable to those of humans. These findings highlight the urgent need to investigate deep-sea exposure pathways and develop effective management strategies.