Rivers in watersheds dominated by agriculture throughout the US are impaired by excess sediment, a significant portion of which comes from non-field, near-channel sources. Both land-use and climate have been implicated in altering river flows and thereby increasing stream-channel erosion and sediment loading. In the wetland-rich landscapes of the upper Mississippi basin, 20th century crop conversions have led to an intensification of artificial drainage, which is now a critical component of modern agriculture. At the same time, much of the region has experienced increased annual rainfall. Uncertainty in separating these drivers of streamflow fuels debate between agricultural and environmental interests on responsibility and solutions for excess riverine sediment. To disentangle the effects of climate and land-use, we compared changes in precipitation, crop conversions, and extent of drained depressional area in 21 Minnesota watersheds over the past 70 years. Watersheds with large land-use changes had increases in seasonal and annual water yields of >50% since 1940. On average, changes in precipitation and crop evapotranspiration explained less than one-half of the increase, with the remainder highly correlated with artificial drainage and loss of depressional areas. Rivers with increased flow have experienced channel widening of 10–40% highlighting a source of sediment seldom addressed by agricultural best management practices. Copyright © 2013 John Wiley & Sons, Ltd.