We compared beaver (Castor canadensis) foraging patterns on Fremont cottonwood (Populus deltoides subsp. wislizenii) saplings and the probability of saplings being cut on a 10 km reach of the flow-regulated Green River and a 8.6 km reach of the free-flowing Yampa River in northwestern Colorado. We measured the abundance and density of cottonwood on each reach and followed the fates of individually marked saplings in three patches of cottonwood on the Yampa River and two patches on the Green River. Two natural floods on the Yampa River and one controlled flood on the Green River between May 1998 and November 1999 allowed us to assess the effect of flooding on beaver herbivory. Independent of beaver herbivory, flow regulation on the Green River has caused a decrease in number of cottonwood patches per kilometre of river, area of patches per kilometre, and average stem density within cottonwood patches. The number of saplings cut per beaver colony was three times lower on the Green River than on the Yampa River but the probability of a sapling being cut by a beaver was still higher on the Green River because of lower sapling density there. Controlled flooding appeared to increase the rate of foraging on the Green River by inundating patches of cottonwood, which enhanced access by beaver. Our results suggest regulation can magnify the impact of beaver on cottonwood through interrelated effects on plant spatial distribution and cottonwood density, with the result that beaver herbivory will need to be considered in plans to enhance cottonwood populations along regulated rivers.