Cadmium (Cd) and its compounds are highly toxic to living organisms and are an environmental health hazard. Rice plants usually accumulate more Cd than other crops; therefore, serious concerns have been raised about human health risks resulting from food webs through Cd-contaminated rice paddy soils since rice is a staple food source for many Asian countries such as China and India. In hilly regions of southern China, rice plants are often cultivated near forests in a forest-rice agroforestry system, where the forests often occupy the upper parts of the hilly areas and the rice paddy fields are often present in the lower parts and in natural depressions. Although forest-rice agroforestry systems have been a typical agricultural model in southern China for many years, the pattern of Cd distribution and cycling and mechanisms controlling its accumulation and transport are still poorly understood in these systems. In this present study, the distribution and dynamic characteristics of Cd were investigated in two types of forest-rice agroforestry systems and one rice paddy system (without forests, as a control) in Taoling Forest Farm, Human Province, China from late May to early September in 2012. The concentration and fluxes of Cd in rainfall water, runoff water, pond water, and rice paddy-field water were measured. The main objectives of this study were to examine the transport patterns of Cd in different components of hydrological process and to calculate input-output budgets of Cd in the forest-rice systems. The results showed that (1) Cd mainly entered into the forest-rice agroforestry systems through precipitation in the study area, much of which happened during the early stage of the rice growing season. (2) Of the total amount of Cd input into the systems by precipitation, about 53% was retained in forests, 7.5% in ponds, 11.6% in rice paddy fields, and 27.9% was exported from the systems through rice paddy-field water, rice-straw, and rice-grain harvesting. (3) Because of the difference in canopy density of forests between the forest-rice agroforestry systems, the mixed forests-rice-paddy system had the highest capacity to retain Cd, followed by the pine forests-rice-paddy system, and the control site had the lowest capacity. It seemed that the retaining capacity of Cd was positively related to the canopy density of forests. (4) The ponds could mitigate the transportation of Cd within the systems, and upper hilly areas had particularly serious soil erosion. (5) Macromolecular organic matter in pond water enhanced the accumulation of Cd in rice paddy fields. The results from the study indicated that the accumulation of Cd was related to Cd concentration in bulk precipitation in forest-rice agroforestry systems. The canopy density of forests and different forest types affected the distribution, transport, and output of Cd in the forest-rice agroforestry systems in the study regions.