Zebra mussels (Dreissena polymorpha) have exacerbated the decline of native freshwater mussels (Order Unionida) in North America since their arrival in the 1980s. Options for controlling invasive mussels, particularly in unionid mussel habitats, are limited. Previously, carbon dioxide (CO2) showed selective toxicity for zebra mussels, relative to unionids, when applied in cool water (12 °C). We first determined 96 h lethal concentrations of CO2 at 5 and 20 °C to zebra mussels and responses of juvenile plain pocketbook (Lampsilis cardium). Next, we compared the time to lethality for zebra mussels at 5, 12, and 20 °C during exposure to partial pressure of CO2 (PCO2) 110¬–120 atmospheres (atm; 1 atm = 101.325 kPa) and responses of juvenile plain pocketbook and fragile papershell (Leptodea fragilis). We found efficacious CO2 treatment regimens at each temperature that were minimally lethal to unionids. At 5 °C, plain pocketbook survived 96 h exposure to the highest PCO2 treatment (139 atm). At 20 °C, the 96 h LC10 (lethal concentration to 10% of animals) for plain pocketbook [173 atm PCO2, 95% confidence interval (CL) 147–198 atm] was higher than the LC99 for zebra mussels (118 atm PCO2, CL 109–127 atm). Lethal time to 99% mortality (LT99) of zebra mussels in 110 to 120 atm PCO2 ranged from 100 h at 20 °C to 300 h at 5 °C. Mean survival of juvenile unionids exceeded 85% in LT99 CO2 treatments at all temperatures. Short-term infusion of 100 to 200 atm PCO2 at a range of water temperatures could reduce biofouling by zebra mussels with limited adverse effects on unionid mussels.