Recent studies suggest that projected rises of aquatic CO 2 levels cause acid-base regulatory responses in fishes that lead to altered GABAergic neurotransmission and disrupted behaviour, threatening fitness and population survival. It is thought that changes in Cl − and HCO 3 − gradients across neural membranes interfere with the function of GABA-gated anion channels (GABA A receptors). So far, such alterations have been revealed experimentally by exposing species living in low-CO 2 environments, like many oceanic habitats, to high levels of CO 2 (hypercapnia). To examine the generality of this phenomenon, we set out to study the opposite situation, hypothesizing that fishes living in typically hypercapnic environments also display behavioural alterations if exposed to low CO 2 levels. This would indicate that ion regulation in the fish brain is fine-tuned to the prevailing CO 2 conditions. We quantified pH regulatory variables and behavioural responses of Pangasianodon hypophthalmus, a fish native to the hypercapnic Mekong River, acclimated to high-CO 2 (3.1 kPa) or low-CO 2 (0.04 kPa) water. We found that brain and blood pH was actively regulated and that the low-CO 2 fish displayed significantly higher activity levels, which were reduced after treatment with gabazine, a GABA A receptor blocker. This indicates an involvement of the GABA A receptor and altered Cl − and HCO 3 − ion gradients. Indeed, Goldman calculations suggest that low levels of environmental CO 2 may cause significant changes in neural ion gradients in P. hypophthalmus. Taken together, the results suggest that brain ion regulation in fishes is fine-tuned to the prevailing ambient CO 2 conditions and is prone to disruption if these conditions change.