This dataset comprises the concentrations of organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs) measured in bed sediments collected from the Forth estuary in Scotland from November 2020 to July 2021, in addition to the north Aberdeenshire coastline in winter 2023. A total of 146 bed sediment surface samples were collected at a range of depths in the water column (2-57 m) in the Forth estuary, and 9 samples in North Aberdeenshire. In the Forth estuary, two sampling areas were selected, specifically the inner estuary channel (sites west of longitude -2.9) and the outer estuary channel (sites east of longitude -2.9). OCs and PBCs were analysed using gas chromatography-mass spectrometry (GC-MS). PBDEs were analysed using gas chromatography-tandem mass spectrometry (GC-MS/MS). These data were collected as part of the Natural Environment Research Council (NERC) funded project entitled "Uptake of chemicals from legacy waste sites in coastal food webs and effects on higher predators" (NERC reference NE/T003596/1). Full details about this dataset can be found at https://doi.org/10.5285/475f098c-dcc4-4e77-b57b-8b9bdeb330a3