© 2016, Springer-Verlag Berlin Heidelberg. The dinoflagellate Symbiodiniumtrenchii associates with a wide array of host corals throughout the world, and its thermal tolerance has made it of particular interest within the context of reef coral resilience to a warming climate. However, future reefs are increasingly likely to face combined environmental stressors, further complicating our understanding of how S. trenchii will possibly acclimatize to future climate scenarios. Over a 33-day period, we characterized the individual and combined affects of high temperature (26.5 vs. 31.5 °C), pCO2 (400 vs. 760 µatm), and elevated nutrients (0.4 and 0.2 vs. 3.5 and 0.3 µmol of NO3/NO2 and PO4 3-, respectively) on S. trenchii within the host coral species Turbinariareniformis. Global analysis across all treatments found temperature to be the largest driver of physiological change. However, exposure to elevated temperature led to changes in symbiont physiology that differed across pCO2 concentrations. Net photosynthesis and cellular chlorophyll a increased with temperature under ambient pCO2, whereas temperature-related differences in cellular volume and its affect on pigment packaging were more pronounced under elevated pCO2. Furthermore, increased nutrients mitigated the physiological response to high temperature under both ambient and elevated pCO2 conditions and represented a significant interaction between all three physical parameters. Individual responses to temperature and pCO2 were also observed as cellular density declined with elevated temperature and calcification along with respiration rates declined with increased pCO2. Symbiodiniumtrenchii remained the dominant symbiont population within the host across all treatment combinations. Our results reveal distinct physiological changes in response to high temperature within the S. trenchii/T. reniformis symbioses that are dependent on pCO2 and nutrient concentration, and represent important interactive effects to consider as we consider how corals will respond under future climate change scenarios.