Heavy-metal contamination of sediments within river systems is a major environmental problem around the world. Deposited as a by-product of metal mining, contaminated sediments are persistent and widespread, frequently affecting large areas of floodplains, which makes precise assessments of contamination levels and patterns difficult. This paper describes findings from a new, generic, catchment sediment model called TRACER, which uses historical mining records to accurately predict present-day and future levels and patterns of contamination. This model provides detailed views of the extent of contamination and demonstrates how contaminated sediments form into “hot spots,” which in turn become secondary sources of pollution. The exceptional longevity of the contamination is also revealed; >70% of the deposited contaminants remain within the river system for >200 yr after mine closure. Simulations of the impact of future climate changes in northern England show that increased flood magnitudes are likely to decrease surface contamination through dilution by cleaner sediment from hillslopes unaffected by mining activity.