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We investigated the distribution of heavy metals Ni, Cu, Zn, As, Cd and Pb in marine sediments in order to evaluate the pollution status in Yowie Bay, in the Port Hacking Estuary, NSW, Australia. Twenty one surface sediments were collected in this study and hydrodynamic parameters (current track and velocity) were also measured in order to explain the distribution of the heavy metals in the bay. Effect Range Low and Effect Range Median statistics were used to assess the environmental effect in order to offer measures to protect the ecosystem from pollution by the accumulation of heavy metals in the bay. The results showed that the heavy metals Ni, Cu, Zn, As, Cd and Pb had similar distribution patterns in surface sediments. The surface sediments were considerably contaminated by copper, cadmium and lead. The highest concentrations of the metals were found to be in the northeast of the bay, which is in close proximity to discharge points and moored watercraft, with the highest reading (sample YO8) having concentrations of 20, 107.4, 304.2, 15, 12.3 and 176.5 ppm, respectively. The heavy metal pollution was concentrated in the inner bay, which has greater depth and contains organic matter and muddy particles (illite, kaolinite and chlorite). The sources of pollution by heavy metals were found to be discharge points and human activities (gasoline fumes, watercraft and boatyards) and this pollution began with European settlement which now surrounds the bay.