Abstract Fish aquaculture facilities strive to maintain abiotic conditions that optimise somatic growth. Two physiological systems that are critically linked to environmental abiotic factors are ion and acid‐base regulation. Given the detrimental effects of ionic and acid‐base imbalances coupled with the potential energetic costs of ion and acid‐base regulation, it is important to understand how changes in abiotic variables such as salinity, temperature and pH alter ionoregulatory and acid‐base physiology. The gill is the predominant site of ion and acid‐base regulation, two linked processes that are vital to the health of fishes. Most species maintain ion levels in the blood plasma within a narrow range, independent of external ion concentrations. In freshwater (FW), fishes must actively take up ions from their dilute environment to counteract passive ion losses, while in seawater (SW), ion excretion serves to counteract passive salt gain. Ion uptake (FW) and excretion (SW) are coordinated by different subtypes of ion‐transporting cells (ionocytes) expressed in the gill epithelium. In this review, we discuss the function of FW and SW ionocytes in the movement of ions across the gill epithelium and address other features of the gill that are integral to ionoregulation. We also discuss the mechanisms of acid‐base regulation by the gill, which is intimately related to ion regulation because it is coordinated by Na + ‐ and Cl − ‐linked fluxes of acid (H + ) and base () equivalents. These fundamental physiological principles are integral in understanding how fishes in aquaculture respond to relevant disturbances that may occur under culture conditions.