Abstract. Soil contamination by trace elements (TEs) is a major concern for sustainable land management. A potential source of excessive inputs of TEs into agricultural soils are organic amendments. Here, we used dynamic simulations carried out with the Intermediate Dynamic Model for Metals (IDMM) to describe the observed trends of topsoil Zn (zinc), Cu (copper), Pb (lead) and Cd (cadmium) concentrations in a long-term (>60-year) crop trial in Switzerland, where soil plots have been treated with different organic amendments (farmyard manure, sewage sludge and compost). The observed ethylenediaminetetraacetic acid disodium salt (EDTA)-extractable concentrations ranged between 2.6 and 27.1 mg kg−1 for Zn, 4.9 and 29.0 mg kg−1 for Cu, 6.1–26.2 mg kg−1 for Pb, and 0.08 and 0.66 mg kg−1 for Cd. Metal input rates were initially estimated based on literature data. An additional, calibrated metal flux, tentatively attributed to mineral weathering, was necessary to fit the observed data. Dissolved organic carbon fluxes were estimated using a soil organic carbon model. The model adequately reproduced the EDTA-extractable (labile) concentrations when input rates were optimised and soil lateral mixing was invoked to account for the edge effect of mechanically ploughing the trial plots. The global average root mean square error (RMSE) was 2.7, and the average bias (overestimation) was −1.66, −2.18, −4.34 and −0.05 mg kg−1 for Zn, Cu, Pb and Cd, respectively. The calibrated model was used to project the long-term metal trends in field conditions (without soil lateral mixing), under stable climate and management practices, with soil organic carbon estimated by modelling and assumed trends in soil pH. Labile metal concentrations to 2100 were largely projected to remain near constant or to decline, except for some metals in plots receiving compost. Ecotoxicological thresholds (critical limits) were predicted to be exceeded presently under sewage sludge inputs and to remain so until 2100. Ecological risks were largely not indicated in the other plots, although some minor exceedances of critical limits were projected to occur for Zn before 2100. This study advances our understanding of TEs' long-term dynamics in agricultural fields, paving the way to quantitative applications of modelling at field scales.