The application of mineral phosphate (P) fertilizers leads to an unintended Cd input into agricultural systems, which might affect soil fertility and quality of crops. The Cd fluxes at three arable sites in Switzerland were determined by a detailed analysis of all inputs (atmospheric deposition, mineral P fertilizers, manure, and weathering) and outputs (seepage water, wheat and barley harvest) during one hydrological year. The most important inputs were mineral P fertilizers (0.49 to 0.57 g Cd ha–1 yr–1) and manure (0.20 to 0.91 g Cd ha–1 yr–1). Mass balances revealed net Cd losses for cultivation of wheat (−0.01 to −0.49 g Cd ha–1 yr–1) but net accumulations for that of barley (+0.18 to +0.71 g Cd ha–1 yr–1). To trace Cd sources and redistribution processes in the soils, we used natural variations in the Cd stable isotope compositions. Cadmium in seepage water (δ114/110Cd = 0.39 to 0.79‰) and plant harvest (0.27 to 0.94‰) was isotopically heavier than in soil (−0.21 to 0.14‰). Consequently, parent material weathering shifted bulk soil isotope compositions to lighter signals following a Rayleigh fractionation process (ε ≈ 0.16). Furthermore, soil-plant cycling extracted isotopically heavy Cd from the subsoil and moved it to the topsoil. These long-term processes and not anthropogenic inputs determined the Cd distribution in our soils.