Ecological risk assessment is increasingly being used to make decisions on the acceptability of industrial processes, as well as on the appropriate approach to take with remediation of contaminated sites. In this approach, the risks and costs must first be determined before decisions can be made. In principle, the procedure for undertaking an ecological risk assessment for a site with existing contamination is fairly straight forward. Probability distributions are obtained for the concentration of the contaminant of concern and for the biological and/or structural impacts likely to occur in the affected habitat. The degree of overlap between these distributions determines the risk from the contaminant to the habitat. With water-borne contamination, the level of assessment can vary from a simple comparison with water quality criteria, through site specific literature surveys, to laboratory and field studies depending on the importance of the environment, the concentration and perceived nature of the contaminant, the resources available, and the likely benefit from the process to be developed. However, a number of uncertainties make this process more difficult. These include the lack of a standard methodology, availability of appropriate data and agreed definitions of acceptable risk. Thus several arbitrary or considered decisions need to be made before and during such an assessment. This paper discusses the application of an ecological risk assessment of copper pollution in Macquarie Harbour, Tasmania, using data from long-term monitoring of waters and literature searches on lethal and sub-lethal effects of copper in marine and estuarine environments. This study is part of a much larger program established to determine best methods for the remediation of the Mt. Lyell copper mine site as well as the freshwater and marine habitats downstream. The results of the assessment indicated that there was at present a probability greater than 0.9 of the occurrence of anodic stripping voltametry-labile copper water concentrations harmful to 5% of all species. For total dissolved copper the probability was higher than 0.98. The upper value of total dissolved copper in Macquarie Harbour that encompassed 90% of the probable concentrations would need to be reduced by a factor of approximately 30, without the inclusion of any additional application factors, to achieve (sub-lethal) protection for 95% of species.