Diagenesis and its effects on the partitioning of trace metals was examined in intertidal muddy sediments in polluted Mangere Inlet, Manukau Harbour, New Zealand. Two cores were sectioned down to 26 cm, and analysed for compounds of Fe, Mn, S, and organic matter. Trace metals were analysed by sequential extraction (nonresidual metals), 0.5M HCl, and XRF (total metals). The sediments were bioturbated, with strong mottling of sediment colour in both cores and intact macropores in one core. Bioturbation appeared to affect sediment chemistry and to cause differences between the cores. There were changes in trace metal partitioning in the non-residual phases with depth, but the changes were relatively small, in line with the changes in major sediment phases. None of the trace metals showed an increase in the lithogenic fraction with depth and we concluded that immobilisation of trace metals by incorporation into residual phases is not an important mechanism in the surface sediments.