Polar cod (Boreogadus saida) is a key species of the arctic food web and links trophic levels. Under ocean acidification (OA), the accumulation of CO2, polar cod exhibits neurochemical alterations as well as behavioural alterations. The underlying factors are still poorly understood. In airbreathing vertebrates, increased CO2 concentrations (hypercapnia) cause increased cerebral blood flow (CBF). Besides potential changes in the blood distribution, elevated environmental CO2 might affect the acid-base status of the brain and its energy metabolism. Therefore, this study aimed to adapt an array of in vivo magnetic resonance imaging (MRI) techniques to investigate potential changes in the blood distribution of the brain of polar cod under OA. To investigate blood flow, phase contrast MRI, FLASH MRI and BOLD imaging were adapted and used under control conditions and conditions of elevated CO2 concentrations. These investigations were complimented by in vivo 31P-NMR spectroscopy to investigate potential changes in intracellular pH and energy metabolism. Fluctuations in blood flow and perfusion were observed but no significant elevations could be identified under OA. OA induced decreases in intracellular pH were subtle and compensated for completely within 24 hours. No substantial alterations in the energy metabolism of the brain were detected under elevated CO2.