Prior to the construction of large dams on the Green and Colorado Rivers, annual floods aggraded sandbars in lateral flow-recirculation eddies with fine sediment scoured from the bed and delivered from upstream. Flows greater than normal dam operations may be used to mimic this process in an attempt to increase time-averaged sandbar size. These controlled floods may rebuild sandbars, but sediment deficit conditions downstream from the dams restrict the frequency that controlled floods produce beneficial results. Here, we integrate complimentary, long-term monitoring data sets from the Colorado River in Marble and Grand Canyons downstream from Glen Canyon dam and the Green River in the Canyon of Lodore downstream from Flaming Gorge dam. Since the mid-1990s, several controlled floods have occurred in these canyon rivers. These controlled floods scour fine sediment from the bed and build sandbars in eddies, thus increasing channel relief. These changes are short-lived, however, as interflood dam operations erode sandbars within several months to years. Controlled flood response and interflood changes in bed elevation are more variable in Marble Canyon and Grand Canyon, likely reflecting more variable fine sediment supply and stronger transience in channel bed sediment storage. Despite these differences, neither system shows a trend in fine-sediment storage during the period in which controlled floods were monitored. These results demonstrate that controlled floods build eddy sandbars and increase channel relief for short interflood periods, and this response may be typical in other dam-influenced canyon rivers. The degree to which these features persist depends on the frequency of controlled floods, but careful consideration of sediment supply is necessary to avoid increasing the long-term sediment deficit.