Globally widespread phosphate fertilizer applications have resulted in long-term increases in the concentration of cadmium (Cd) in soils. The accumulation of this biotoxic, and bioaccumulative metal presents problems for the management of soil-plant-animal systems, because the magnitude and direction of removal fluxes (e.g., crop uptake, leaching) have been difficult to estimate. Here, Cd isotopic compositions (δ¹¹⁴/¹¹⁰Cd) of archived fertilizer and soil samples from a 66 year-long agricultural field trial in Winchmore, New Zealand, were used to constrain the Cd soil mass balance between 1959 and 2015 AD, informing future soil Cd accumulation trajectories. The isotopic partitioning of soil Cd sources in this system was aided by a change in phosphate source rocks in 1998 AD, and a corresponding shift in fertilizer isotope composition. The dominant influence of mixing between isotopically distinct Cd end-members was confirmed by a Bayesian modeling approach. Furthermore, isotope mass balance modeling revealed that Cd removal processes most likely increased in magnitude substantially between 2000 and 2015 AD, implying an increase in Cd bioaccumulation and/or leaching over that interval. Natural-abundance stable isotopes are introduced here as a powerful tool for tracing the fate of Cd in agricultural soils, and potentially the wider environment.