In addition to causing physical degradation and nutrient depletion, erosion of cultivated soils in the Amazon affects aquatic ecosystems through the release of natural soil mercury (Hg) towards lakes and rivers. While traditional agriculture is generally cited as being among the main causes of soil erosion, agroforestry practices are increasingly appreciated for soil conservation. This study was carried out in family farms of the rural Tapajós region (Brazil) and aimed at evaluating soil erosion and associated Hg release for three land uses. Soils, runoff water and eroded sediments were collected at three sites representing a land cover gradient: a recently burnt short-cycle cropping system (SCC), a 2-year-old agroforestry system (AFS) and a mature forest (F). At each site, two PVC soil erosion plots (each composed of three 2 × 5 m isolated subplots) were implemented on steep and moderate slopes respectively. Sampling was done after each of the 20 rain events that occurred during a 1-month study period, in the peak of the 2011 rain season. Runoff volume and rate, as well as eroded soil particles with their Hg and cation concentrations were determined. Total Hg and cation losses were then calculated for each subplot. Erosion processes were dominated by land use type over rainfall or soil slope. Eroded soil particles, as well as the amount of Hg and cations (CaMgK) mobilized at the AFS site were similar to those at the F site, but significantly lower than those at the SCC site (p < 0.0001). Erosion reduction at the AFS site was mainly attributed to the ground cover plants characterizing the recently established system. Moreover, edaphic change throughout AFS and F soil profiles differed from the SCC site. At the latter site, losses of fine particles and Hg were enhanced towards soil surface, while they were less pronounced at the other sites. This study shows that agroforestry systems, even in their early stages of implementation, are characterized by low erosion levels resembling those of local forest environments, thus contributing to the maintenance of soil integrity and to the reduction of Hg and nutrient mobility.