Fremont cottonwood (Populus fremontii) is an early successional foundation species found in riparian forest ecosystems in the North American Southwest. Along rivers, the upper limit of the seedling establishment zone depends on the proximity of seedling roots to the declining water table. The lower limit is a function of the maximum elevation of inundation or scour. Fremont cottonwood seedlings are likely to experience short-term (1- to 5-week) inundation during their first year of growth under both natural and human-influenced hydrologic regimes. Previous studies show that inundation can account for more than 70% of seedling mortality during this time. Using controlled inundation experiments, we found that seedlings of Fremont cottonwood have high tolerance of inundation to the soil surface and a reasonable tolerance of complete shoot submergence for a duration of 1 or 2 weeks (22% and 50% mortality, respectively). Mortality increased linearly with days of complete submergence (mortality percentage = 4.6 [2.5 × days of submergence]). Warm water temperature (25/18 °C day/night) during complete submergence adversely affected seedling biomass and survival, resulting in 64% mortality versus 39% with cooler water temperatures (18/11 °C day/night). Our results indicate that establishment of new Fremont cottonwood populations in the riparian corridor will be more successful when flows do not completely cover the shoots of seedlings for more than 2 weeks and if water temperatures during inundation are cool. From the perspective of the management of river flows for cottonwood recruitment, deep, prolonged, late-season (warm water) inundations are the most detrimental.