Agricultural soil loss and deposition in aquatic ecosystems is a problem that impairs water quality worldwide and is costly to agriculture and food supplies. In the US, for example, billions of dollars have subsidized soil and water conservation practices in agricultural landscapes over the past decades. We used paleolimnological methods to reconstruct trends in sedimentation related to human-induced landscape change in 32 lakes in the intensively agricultural region of the Midwestern United States. Despite erosion control efforts, we found accelerating increases in sediment deposition from erosion; median erosion loss since 1800 has been 15.4 tons ha-1. Sediment deposition from erosion increased >6-fold, from 149 g m-2 yr-1 in 1850 to 986 g m-2 yr-1 by 2010. Average time to accumulate one mm of sediment decreased from 631 days before European settlement (ca. 1850) to 59 days mm-1 at present. Most of this sediment was deposited in the last 50 years and is related to agricultural intensification rather than land clearance or predominance of agricultural lands. In the face of these intensive agricultural practices, traditional soil conservation programs have not decelerated downstream losses. Despite large erosion control subsidies, erosion and declining water quality continue, thus new approaches are needed to mitigate erosion and water degradation.