Climate change is expected to increase the frequency of intense flooding events, and thus the risk of flood-related mortality, infrastructure damage, and economic loss. Assessments of future flooding from global climate models based only on precipitation intensity and temperature neglect important processes that occur within the land-surface, particularly the impacts of plant-physiological responses to rising CO₂. Higher CO₂ reduces stomatal conductance, leading to less water loss through transpiration and higher soil moisture. For a given precipitation rate, higher soil moisture decreases the amount of rainwater that infiltrates the surface and increases runoff. Here we assess the relative impacts of plant-physiological and radiative-greenhouse effects on changes in extreme runoff intensity over tropical continents using the Community Earth System Model. We find that extreme percentile rates increase significantly more than mean runoff in response to higher CO₂. Plant-physiological effects contribute to only a small increase in precipitation intensity, but are a dominant driver of runoff intensification, contributing to one-half of the 99th percentile runoff intensity change and one-third of the 99.9th percentile change. Comprehensive assessments of future flooding risk need to account for the physiological as well as radiative impacts of CO₂ in order to better inform flood prediction and mitigation practices.