Energetic costs associated with ion and acid-base regulation in response to ocean acidification have been predicted to decrease the energy available to fish for basic life processes. However, the low cost of ion regulation (6–15% of standard metabolic rate) and inherent variation associated with whole-animal metabolic rate measurements have made it difficult to consistently demonstrate such a cost. Here we aimed to gain resolution in assessing the energetic demand associated with acid-base regulation by examining ion movement and O 2 consumption rates of isolated intestinal tissue from Gulf toadfish acclimated to control or 1900 μatm CO 2 (projected for year 2300). The active marine fish intestine absorbs ions from ingested seawater in exchange for HCO 3 − to maintain water balance. We demonstrate that CO 2 exposure causes a 13% increase of intestinal HCO 3 − secretion that the animal does not appear to regulate. Isolated tissue from CO 2-exposed toadfish also exhibited an 8% higher O 2 consumption rate than tissue from controls. These findings show that compensation for CO 2 leads to a seemingly maladaptive persistent base (HCO 3 −) loss that incurs an energetic expense at the tissue level. Sustained increases to baseline metabolic rate could lead to energetic reallocations away from other life processes at the whole-animal level.