River flow reconstructions are typically developed using tree rings from montane conifers that cannot reflect flow regulation or hydrologic inputs from the lower portions of a watershed. Incorporating lowland riparian trees may improve the accuracy of flow reconstructions when these trees are physically linked to the alluvial water table. We used riparian plains cottonwoods (Populus deltoides ssp. monilifera) to reconstruct discharge for three neighboring rivers in the Upper Missouri River Basin: the Yellowstone (n = 389 tree cores), Powder (n = 408), and Little Missouri Rivers (n = 643). We used the Regional Curve Standardization approach to reconstruct log-transformed discharge over the 4 months in early summer that most highly correlated to tree ring growth. The reconstructions explained at least 57% of the variance in historical discharge and extended back to 1742, 1729, and 1643. These are the first flow reconstructions for the Lower Yellowstone and Powder Rivers, and they are the furthest downstream among Rocky Mountain rivers in the Missouri River Basin. Although mostly free-flowing, the Yellowstone and Powder Rivers experienced a shift from early-summer to late-summer flows within the last century. This shift is concurrent with increasing irrigation and reservoir storage, and it corresponds to decreased cottonwood growth. Low-frequency flow patterns revealed wet conditions from 1870 to 1980, a period that includes the majority of the historical record. The 1816–1823 and 1861–1865 droughts were more severe than any recorded, revealing that drought risks are underestimated when using the instrumental record alone.