In the Alberta oil sands region, insufficient knowledge of pre-disturbance reference conditions has undermined the ability of the Regional Aquatics Monitoring Program (RAMP) to detect pollution of the Athabasca River, because sampling began three decades after the industry started and the river naturally erodes oil-bearing strata. Here, we apply a novel approach to characterize pre-industrial reference metal concentrations in river sediment downstream of Alberta oil sands development by analyzing metal concentrations in sediments deposited in floodplain lakes of the Athabasca Delta during 1700–1916, when they were strongly influenced by Athabasca River floodwaters. We compared results to metal concentrations in surficial bottom sediments sampled by RAMP (2010–2013) at downstream sites of the Athabasca River and distributaries.