- The effect of three seawater CO2 concentrations (0.8 ± 0.18, 5.64 ± 0.64 and 28.58 ± 3 mg l− 1), was tested on white grouper (Epinephelus aeneus) post-larvae reared at two water temperatures (23 and 27 °C) in a 30 aquarium (17 l each) experimental system. Forty-five dph fish were stocked per aquarium allowing the testing of the 6 CO2 temperature treatment combinations in replicates of 5 aquaria treatment− 1 for 60 days. 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 ± 0.18 mg l− 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 ± 3 mg l− 1) at 23 °C. Following the 60 days of the CO2 and temperature exposure period (45–105 dph), 87–100% of the fish from the six treatment combinations, independent of temperature and CO2 exposure history, had inflated swimbladders at 150 dph. It was shown that, during the recovery phase (125 dph) at 23 °C, the ratio between the swimbladder volume and body weight (mm3 g− 1) in fish exposed to the high CO2 concentration was 4.65 ± 0.79 mm3 g− 1, which was significantly smaller (P < 0.05) than 10.12 ± 0.72 mm3 g− 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.