Lake Macquarie, an estuarine lake on Australia's eastern seaboard, has been subject for almost a century to anthropogenic contamination by heavy metals and metalloids, including selenium, arising from industrial sources including a lead-zinc smelter, coal-fired power stations and sewage works. , Selenium tissue concentrations in fish from the Lake have recently been reported at up to twelve times those recommended for human consumption. This paper describes an integrated investigation into selenium contamination in the Lake over a four-year period. One key component of these investigations is the ability of indigenous micro-organisms to reduce selenium in estuarine sediments from higher to lower oxidation states, therefore immobilising or volatilising it, and the use of this in the treatment of industrial wastewaters or potentially the in-situ bioremediation of contaminated sediments. A second key component is a study of the mechanisms controlling sediment-stored selenium concentrations and the extent to which they can be influenced by bioturbative organisms. Integrated into these two broad areas and described here are a number of related investigations into: bioavailability of sediment-bound selenium; computer modelling of selenium biogeochemistry; representation of heavy metal data in a GIS format; and determination of the specific historical contributions of a power station to selenium loads in the Lake. Through this integrated approach we have built on synergies between the separate components of our research program to add to our understanding of the nature of selenium biogeochemistry in the Lake and to propose potential bioremediation strategies for both the Lake and contaminated industrial wastewaters or surface water.