Metal impacted, anoxic sediments from five sites at a coastal location in the wet/dry tropics of Australia were sampled during both wet and dry seasons. Metal concentrations in total sediment and porewater, and in potentially bioavailable and bioaccessible fractions, were measured. Pyrosequencing was used to sequence bacterial DNA extracted from the sediment, and the sequence data was used to generate community profiles at each sample site. Changes in bacterial populations between sites reflected changes in the concentrations of 7 metals/metalloids (Al, V, Mo, Ga, Zn, Cd, As), and best correlated with the HCl-extractable fraction of metals. Bacterial community structure was also related to physicochemical factors, such as redox potential and organic carbon. Despite a strong sulphide gradient across the transect, acid-volatile sulphide was not significantly correlated to bacterial community structure. We conclude that the bioaccessible fraction of metals to bacteria is partly comprised of particulates, and porewater alone is not a sufficient model for potential metal impact.[Supplementary materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the two supplementary tables.].