From 1985 onwards, South America has undergone a major expansion in agriculture at the expense of native vegetation (for example, native Pampa grassland). As an emblematic crop, the surface area cultivated with soybeans has increased by 1,000% between 1990 and 2020 in Uruguay. The environmental consequences of this massive land-use conversion on soil degradation remain poorly documented, although agriculture expansion is projected to continue to increase in the coming years in South America. In this study, sediment cores were collected in reservoirs located downstream of two contrasted agricultural catchments draining the Rio Negro River (Uruguay) to reconstruct the sediment dynamics and the sources of erosion associated with this expansion. Results demonstrated the occurrence of two periods of acceleration of sediment delivery since the 1980s. The first period of acceleration was recorded in the mid-1990s and was related to afforestation programs. The second and larger acceleration phase was recorded after 2000 during the soybean crop expansion. This period was marked by a greater supply of sediment from the native grassland source, highlighting the impact of agriculture expansion at the expense of native vegetation. Conservation measures should therefore be urgently taken to preserve biodiversity and soil functions in this region. The impacts on soil degradation of the massive land-use conversion of South American Pampa grasslands to agriculture are not well documented. This study estimates, over the period 1982–2019, the impacts of such conversion on the sediment cascade and how soil and water resources are affected as a result.