The effect of three seawater CO2 concentrations (0.8±0.18, 5.64±0.64 and 28.58±3mgl−1), was tested on white grouper (Epinephelus aeneus) post-larvae reared at two water temperatures (23 and 27°C) in a 30 aquarium (17l each) experimental system. Forty-five dph fish were stocked per aquarium allowing the testing of the 6 CO2 temperature treatment combinations in replicates of 5aquariatreatment−1 for 60days. The final weight of fish reared under the high CO2 treatment was 25% and 10% (P<0.05) lower than that of fish reared under the control conditions at 23° and 27°C, respectively. A similar pattern in total length (TL) was demonstrated where fish exposed to the high CO2 treatment grew 10 and 7.4% more slowly (P<0.05) than the control at 23° and 27°C, respectively. A large percentage (78.8±6.1%) of fish reared at the control CO2 concentration (0.8±0.18mgl−1) and exposed to 27°C had inflated swimbladders compared to only 17.6±9.2% in fish exposed to the high CO2 concentration (28.58±3mgl−1) at 23°C. Following the 60days of the CO2 and temperature exposure period (45–105dph), 87–100% of the fish from the six treatment combinations, independent of temperature and CO2 exposure history, had inflated swimbladders at 150dph. It was shown that, during the recovery phase (125dph) at 23°C, the ratio between the swimbladder volume and body weight (mm3g−1) in fish exposed to the high CO2 concentration was 4.65±0.79mm3g−1, which was significantly smaller (P<0.05) than 10.12±0.72mm3g−1in the control CO2 treatment. In general, the swimbladder volume was directly correlated with the rearing temperature and was up to 50% larger in fish reared at 27°C compared to those from 23°C independent of CO2 concentration. The relative presence of skeletal deformities in fish with non-inflated swimbladders was 6.49%, which was significantly (P<0.05) higher than the 0.93% in fish with a normally inflated swimbladder. In addition, fish with an uninflated swimbladder demonstrated a significantly (P<0.05) more severe lordosis deformity with a vertebra angle of 47.5±15° compared to cohorts with an inflated swimbladder that exhibited an angle of 27±6°. In conclusion, there was a clear effect of high aqueous levels of CO2 and environmental temperature on growth and skeletal deformity which, in turn, affected juvenile quality in the white grouper.