The aim of this study is to assess the annual balance of the fluxes of Cd, Cu, Ni, Pb and Zn within different cropping systems, in an experimental site located near Versailles, France. Four fluxes through the cultivated horizon were considered to assess the annual heavy metal balance in these systems: 1) atmospheric depositions, 2) fertilisers as inputs, 3) crops and 4) leaching water as outputs. The water mass flow was estimated with a model (CERES) while the other parameters were actually measured through field sampling. Some large uncertainties are related to analytical detection limits, specially for Pb which presents very low concentrations in nitrogen fertilisers, in crops and in soil solution. Cd was also close to the detection limits in atmospheric deposition and in soil water, and Zn could not be analysed in soil solution. Nevertheless, the following trends clearly appeared: firstly, atmospheric deposition is the major input way of Cu, Ni, Pb and Zn in the soil, whatever the cropping system, whereas Cd is introduced mainly by fertilisers. Secondly, the uptake of heavy metal by wheat is generally larger than by a pea culture, except for Ni. Finally, the global pattern shows an accumulation of Cd, Ni and Pb in the cultivated horizon while Cu decreased. The annual balances, during the cropping year 2001–2002, represented about 0.33, −0.024, 0.014 and 0.014% of the actual stocks in the cultivated horizon, of Cd, Cu, Ni, and Pb, respectively.