Concentrations of arsenic, nickel and chromium in sediments of the nearshore Pilbara Region of Western Australia's mid-north coast have caused concerns to regulators issuing ocean disposal permits for many years. A meta-analysis of data from a large number of surveys, conducted in support of permit applications over many years and across hundreds of kilometres of coastline, shows that, when assessed as total metal concentrations, chromium and nickel occur routinely at concentrations above those recommended as screening triggers by national guidelines and arsenic more rarely. Arsenic was concentrated in surface sediments, consistent with an organic origin. Concentrations of nickel and chromium were higher in deeper sediment layers, consistent with a natural geological origin. However, sediment particle sizing was a major determinant of total metal concentrations of all three metals, and bioavailability was always much lower and within recommended guidelines. Past dredging activity for channels and berths in the large ports of the Pilbara has most likely led to an elevation of fine fractions of surface sediments within operating port areas, when compared to the undisturbed surrounding areas, and may also have increased the proportion of sediment from deeper substrates at the surface. Whilst total concentrations of chromium and nickel commonly exceed screening guidelines throughout the nearshore Pilbara Region, their bioavailability was low and these metals present a little threat to biota.