Effects of agricultural land management practices on surface runoff are evident at local scales, but evidence for watershed-scale impacts is limited. In this study, we used the Soil and Water Assessment Tool model to assess changes in downstream flood risks under different land uses for the large, intensely agricultural, Raccoon River watershed in Iowa. We first developed a baseline model for flood risk based on current land use and typical weather patterns and then simulated the effects of varying levels of increased perennials on the landscape under the same weather patterns. Results suggest that land use changes in the Raccoon River could reduce the likelihood of flood events, decreasing both the number of flood events and the frequency of severe floods. The duration of flood events were not substantially affected by land use change in our assessment. The greatest flood risk reduction was associated with converting all cropland to perennial vegetation, but we found that converting half of the land to perennial vegetation or extended rotations (and leaving the remaining area in cropland) could also have major effects on reducing downstream flooding potential. We discuss the potential costs of adopting the land use change in the watershed to illustrate the scale of subsidies required to induce large-scale conversion to perennially based systems needed for flood risk reduction. Copyright © 2013 John Wiley & Sons, Ltd.