The studies of heavy metal input and output fluxes from farmland soils will contribute to sustainable agricultural practices. However, debate on the primary pollution to crops has not resulted in the emergence of practical remediation strategies. Hence, the flux should be identified with precision for targeted pollution control. In this study, a catchment downstream of a metal mining area was selected for investigation of Cadmium pollution in the topsoil of farmlands, including the input and output fluxes in different environmental media. The results showed that irrigation was the main input source of Cd to soil, accounting for more than 75%, in which the contribution of dissolved Cd in water was 1–2 orders of magnitude higher than that of Cd adsorbed on suspended particles. Crop harvesting, surface runoff, and leaching were the main Cd output pathways from this area. The dynamic prediction results under different scenarios showed that Cd in farmland soil would be in a cumulative state in the following years by 2050. Straw removing could significantly reduce Cd accumulation in farmland soil. In addition, the substantial increase of crop yield in the future would increase the Cd output flux. This work revealed the accumulation pattern of Cd in farmland soils, and will aid in the development of remediation strategies for cadmium contamination of agricultural soils.