The control of heavy metals in such a way that soil functioning and product quality are not impeded is a prerequisie to sustainable agricutture. The current status of heavy metal accumulation in agricultural soils differs widely by region, by metal, and by agricultural system; levels of concern have already been reached in several regions (for instance, in the Netherlands and Australia). An analysis of the input and output fluxes of cadmium (Cd), copper (Cu), lead (Pb), and zinc (Zn) in agriculture and of their resulting accumulation in agricultural soils is necessary to define strategies that ensure sustainable management of these metals in agricultural systems. In this article, general aspects of heavy‐metal balance studies are described for the agricultural sector within the broader context of substance flow analysis and industrial ecology. The approach chosen in this study is both precautionary and related to actual problem areas.