Waterways in the Southern Hemisphere, including on the Australian continent, are facing increasing levels of mercury contamination due to industrialization, agricultural intensification, energy production, urbanization, and mining. Mercury contamination undermines the use of waterways as a source of potable water and also has a deleterious effect on aquatic organisms. When developing management strategies to reduce mercury levels in waterways, it is crucial to set appropriate targets for the mitigation of these contaminated waterways. These mitigation targets could be (1) trigger values or default guideline values provided by water and sediment quality guidelines or (2) background (pre-industrialization) levels of mercury in waterways or sediments. The aims of this study were to (1) quantify the differences between existing environmental guideline values for mercury in freshwater lakes and background mercury concentrations and (2) determine the key factors affecting the spatial differences in background mercury concentrations in freshwater lake systems in Australia. Mercury concentrations were measured in background sediments from 21 lakes in Australia. These data indicate that background mercury concentrations in lake sediments can vary significantly across the continent and are up to nine times lower than current sediment quality guidelines in Australia and New Zealand. This indicates that if waterway managers are aiming to restore systems to ‘pre-industrialization’ mercury levels, it is highly important to quantify the site-specific background mercury concentration. Organic matter and precipitation were the main factors correlating with background mercury concentrations in lake sediments. We also found that the geology of the lake catchment correlates to the background mercury concentration of lake sediments. The highest mercury background concentrations were found in lakes in igneous mafic intrusive regions and the lowest in areas underlain by regolith. Taking into account these findings, we provide a preliminary map of predicted background mercury sediment concentrations across Australia that could be used by waterway managers for determining management targets.