The physiological effects of high CO2 concentrations, i.e., [CO2], on plant stomatal responses may be of major importance in understanding the consequences of climate change, by causing increases in runoff through suppression of plant transpiration. Radiative forcing by high [CO2] has been the main consideration in models of global change to the exclusion of plant physiological forcing, but this potentially underestimates the effects on the hydrological cycle, and the consequences for ecosystems. We tested the physiological responses of fossil plants from the Triassic–Jurassic boundary transition (Tr–J) succession of East Greenland. This interval marks a major high CO2-driven environmental upheaval, with faunal mass extinctions and significant floral turnover. Our results show that both stomatal size (expressed in fossil material as SL, the length of the stomatal complex opening) and stomatal density (SD, the number of stomata per mm2) decreased significantly during the Tr–J. We estimate, using a leaf gas-exchange model, that the decreases in SD and SL resulted in a 50%–60% drop in stomatal and canopy transpiration at the Tr–J. We also present new field evidence indicating simultaneous increases in runoff and erosion rates. We propose that the consequences of stomatal responses to elevated [CO2] may lead to locally increased runoff and erosion, and may link terrestrial and marine biodiversity loss via the hydrological cycle.