1. The structure and functioning of riverine ecosystems is dependent upon regional setting and the interplay of hydrologic regime and geomorphologic processes. We used a retrospective analysis to study recruitment along broad, alluvial valley segments (parks) and canyon segments of the unregulated Yampa River and the regulated Green River in the upper Colorado River basin, USA. We precisely aged 811 individuals of Populus deltoides ssp. wislizenii (native) and Tamarix ramosissima (exotic) from 182 wooded patches and determined the elevation and character of the germination surface for each. We used logistic regression to relate recruitment events (presence or absence of cohort) to five flow and two weather parameters.

2. Woody plant establishment occurred via multiple pathways at patch, reach and segment scales. Recruitment occurred through establishment on (1) vertically accreting bars in the unregulated alluvial valley, (2) high alluvial floodplain surfaces during rare large flood events, (3) vertically accreting channel margin deposits in canyon pools and eddies, (4) vertically accreting intermittent/abandoned channels, (5) low elevation gravel bars and debris fans in canyons during multi-year droughts, and (6) bars and channels formed prior to flow regulation on the dammed river during controlled flood events.

3. The Yampa River's peak flow was rarely included in models estimating the likelihood that recruitment would occur in any year. Flow variability and the interannual pattern of flows, rather than individual large floods, control most establishment.

4. Regulation of the Green River flow since 1962 has had different effects on woody vegetation recruitment in canyons and valleys. The current regime mimics drought in a canyon setting, accelerating Tamarix invasion whereas in valleys the ongoing geomorphic adjustment of the channel, combined with reduced flow variability, has nearly eliminated Populus establishment.

5. A single year's flow or a particular pattern of flows over a sequence of years, whether natural or man-made, produces different recruitment opportunities in alluvial and canyon reaches, in diverse landforms within a particular river reach, and for Populus and Tamarix. The design of flows to restore riparian ecosystems must consider these multiple pathways and adjust the seasonal timing, magnitude and interannual frequency of flows to match the desired outcome.