Isoprene is emitted from leaves of numerous plant species and has important implications for plant metabolism and atmospheric chemistry. The ability to use stored carbon (alternative carbon sources), as opposed to recently assimilated photosynthate, for isoprene production may be important as plants routinely experience photosynthetic depression in response to environmental stress. A CO2-labelling study was performed and stable isotopes of carbon were used to examine the role of alternative carbon sources in isoprene production in Populus deltoides during conditions of water stress and high leaf temperature. Isotopic fractionation during isoprene production was higher in heat- and water-stressed leaves (−8.5 and −9.3‰, respectively) than in unstressed controls (−2.5 to −3.2‰). In unstressed plants, 84–88% of the carbon in isoprene was derived from recently assimilated photosynthate. A significant shift in the isoprene carbon composition from photosynthate to alternative carbon sources was observed only under severe photosynthetic limitation (stomatal conductance < 0.05 mol m−2 s−1). The contribution of photosynthate to isoprene production decreased to 77 and 61% in heat- and water-stressed leaves, respectively. Across water- and heat-stress experiments, allocation of photosynthate was negatively correlated to the ratio of isoprene emission to photosynthesis. In water-stressed plants, the use of alternative carbon was also related to stomatal conductance. It has been proposed that isoprene emission may be regulated by substrate availability. Thus, understanding carbon partitioning to isoprene production from multiple sources is essential for building predictive models of isoprene emission.