Ocean acidification (OA) is predicted to affect the physiology of some fishes. To date, most studies have investigated this issue using stable pCO2 levels based on open ocean projections. Yet, most shallow, nearshore systems experience temporal and spatial pCO2 fluctuations. For example, pCO2 on coral reefs is highest at night and lowest during the day, but as OA progresses, both the average pCO2 and magnitude of fluctuations are expected to increase. We exposed four coral reef fishes – Lutjanus fulviflamma, Caesio cuning, Abudefduf whitleyi, and Cheilodipterus quinquelineatus – to ambient, stable elevated, or fluctuating elevated pCO2 conditions for 9–11 days. Then, we measured swimming performance, oxygen uptake rates, and haematological parameters during the day and at night. When compared to ambient pCO2 conditions, L. fulviflamma, C. cuning, and A. whitleyi exposed to fluctuating elevated pCO2 increased swimming performance, maximum oxygen uptake rates, and aerobic scope, regardless of time of day; whereas, the only nocturnal species studied, C. quinquelineatus, decreased maximum oxygen uptake rates and aerobic scope. Our findings suggest that exposure to fluctuating or stable elevated pCO2 can physiologically benefit some coral reef fishes; however, other species, such as the cardinalfish examined here, may be more sensitive to future OA conditions.