When assigning site-specific restoration targets for deteriorating aquatic systems, it is necessary to have an understanding of the undisturbed or background state of the system. However, the site-specific characteristics of aquatic systems prior to disturbance are mostly unknown, due to the lack of historical water and sediment quality data. This study aims to introduce a method for filling this gap in our understanding, using dated sediment cores from the beds of aquatic environments. We used Bolin Billabong, a floodplain lake of the Yarra River (South-East Australia), as a case study to demonstrate the application of this method. We identified the concentrations of aluminium, cadmium, chromium, copper, iron, lead, manganese, nickel, tin and zinc at 8 cm intervals through the sediment core. This showed that aluminium, chromium, copper, iron, lead, nickel, tin and zinc concentrations in Bolin Billabong sediments significantly increased after European settlement in the river catchment in the mid-19th century. The differences between current Australian sediment quality guidelines trigger values and the background metal concentrations in Bolin Billabong sediments underscore the value of using locally relevant background toxicant concentrations when setting water and sediment quality targets.