The shift from rural lifestyles to urban living has dramatically altered the way humans interact and live across the globe. With over 50% of the world’s populations living within cities, and significant increases expected over the next 50 years, it is critical that changes to social, economic and environmental sustainability of cities globally be implicit. Protecting and enhancing aquatic ecosystems, which provide important ecosystem services, is challenging. A number of factors influence pollutants in urban waterways including changes in land-use, impervious area and stormwater discharges, with sediment-bound pollution a major issue worldwide. This work aimed to investigate the spatial and temporal distribution of trace metals in freshwater sediments from six urbanised catchment over a 30-year period. It provides an estimate of pollution using a geoaccumulation index and examines possible toxicity using a probable effect concentration quotient (mPECq). Results showed significant temporal changes in metal concentrations over time, with lead generally decreasing in all but one of the sites, attributed to significant changes in environmental policies and the active elimination of lead products. Temporal changes in other metals were variable and likely dependent on site-specific factors. While it is likely that diffuse pollution is driving changes in zinc, for metals such as lead, chromium and copper, it is likely that watershed landuse and/or point sources are more important. The results clearly indicated that changes to watershed landuse, environmental policy and pollution abatement programs are all driving changes in sediment quality, highlighting the utility of long-term sediment monitoring for assessment of urban watershed condition. While this study has demonstrated the utility of detecting long-term changes in metal concentrations, this approach could easily be adapted to detect and assess future trends in other hydrophobic contaminants and emerging chemicals of concern, such as synthetic pyrethroids, providing essential information for the protection of catchment.