Water supply is a limited resource in most salmon hatcheries, which is compensated by reduced water flow and oxygenation. However, reduced water exchange can lead to accumulation of CO2, resulting in environmental hypercapnia, which may have negative impacts on fish welfare. Thus, environmental hypercapnia can be a common welfare problem for salmon in hatcheries, and particularly in recirculating systems (RAS).In this experiment, Atlantic salmon were exposed to chronic environmental hypercapnia during the last 68 days of the freshwater phase, whereupon effects on physiological stress coping mechanisms and morphological welfare indicators were investigated. Effects on stress coping mechanisms were quantified by measuring changes in brain serotonergic chemistry and plasma cortisol at basal levels and in response to a standardized acute stress test. The results show that exposure to elevated CO2 saturation in the water compromised stress responsiveness of brainstem serotonergic activity, altered osmotic homeostasis, and suppressed growth indicating that fish experience allostatic overload. However, no effects on morphological welfare indicators were observed. This accentuates the need for physiological measures, including physiological responses to controlled challenges to activate the stress axis, when investigating the welfare status of fish reared in systems with potential high CO2.