Land-use changes affect hydrologic processes, but their impact on flooding remains obscure amid increasingly heavy precipitation. Instrumental records are short relative to land-use change history and inadequate for flood attribution studies. Here we integrate a high-resolution paleodischarge record spanning the past ~200 years from the largest basin in the Southeastern United States with instrumental data and hydrological modeling. We find that the 100-yr flood magnitude for large regional rivers exhibits 50–75% reductions in the mid-20th century. We attribute at least 50% of the reductions to a regional shift from widespread agricultural land to conservation and reforestation and the rest to streamflow regulations. A sensitivity test of the largest post-1950s flood in our study area using the WRF-Hydro model shows that the peak early-1900s agriculture activity in the region could have doubled the flood’s magnitude. Our findings suggest that land-use change can profoundly impact flood severity at catchment to regional scales. Therefore, reforestation and soil conservation contribute to alleviating flood hazard in some regions, while aggressive agriculture expansion in other areas will amplify the hazard.