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Trace metal flux measurements in low-contamination agricultural soils are rare, particularly leaching fluxes and atmospheric deposition. Over three years, Cd, Cr, Cu, Ni, Pb, and Zn fluxes in soils at two agricultural sites in north-eastern France were estimated by quantifying and analysing atmospheric deposition, fertilizers, amendments, pesticides, crops, and water percolating at a depth of 80 cm. The La Bouzule site included three soil types cultivated identically and receiving anaerobic digestate. At Haroué, two low-input cropping systems were compared. Atmospheric deposition is in the order of rural background noise. Trace metal concentrations in percolating water were very low, likely due to the alkalinity of the soils. These were often much lower than those estimated by the pedotransfer functions used to predict leaching fluxes. The flux balances were positive for all trace metals and soils because the outputs through leaching and harvest were low. These varied by a factor of nearly 1000 depending on the element, as did the inputs. The highest balance was for Zn and the lowest for Cd. Trace metal inputs with organic pesticide and mineral nitrogen fertilizers were negligeable. In the low-input system, atmospheric deposition, although relatively low was the main contributor to soil metal enrichment, although this would appear to be slight over the long term. Where agricultural inputs were higher, due to the spreading of anaerobic digestate (La Bouzule), long-term soil enrichments in Cd, Cu, and Zn can be expected. Similar measurements should be made in other cropping systems with different soils and agricultural inputs. • The flux balances were positive for all trace metals • They varied by a factor of nearly 1000 depending on the element, as did the inputs • Pedotransfer functions overestimated trace metal contents in percolating water