The preservation of ion balance and pH despite environmental fluctuations is essential for the maintenance of vital cellular functions. While several ion transporters contribute to acid-base regulation in fish, the involvement and expression of key transporters under hypercapnia remains to be established. Here, two members of the HCO₃^--transporter family (Na⁺/HCO₃^--cotransporter: NBC1; Cl^-/HCO₃^--exchanger: AE1) were described for the first time in gills of marine fish. Benthic eelpout Zoarces viviparus were acclimated to 10,000 ppm CO₂. Hypercapnia did not affect whole animal oxygen consumption over a period of four days. During a time series of 6 weeks NBC1 mRNA levels first decreased by about 40 % (8 to 24 h), but finally increased about threefold over control. mRNA expression of AE1 decreased transiently by 50 % at day 4, but recovered to control levels only. Reduced mRNA levels were also found for two Na⁺/H⁺-exchangers (NHE1A, NHE1B) during the first days (by 50 - 60 % at day 1/2), followed by restoration of control levels. This pattern was mirrored in a slight decrease of NHE1 protein contents and its subsequent recovery. In contrast, Na⁺/K⁺-ATPase mRNA and protein contents, as well as maximum activity rose steadily from the onset of hypercapnia, and reached up to twofold control levels at the end. These results indicate shifting acclimation patterns between short and long-term CO₂ exposures. Overall, ion gradient dependent transporter mRNA levels were transiently downregulated in the beginning of the disturbance. Upregulation of NBC1 on long timescales stresses the importance of this transporter in the hypercapnia response of marine teleosts. Long-term rearrangements include Na⁺/K⁺-ATPase at higher densities and capacities indicating a shift to elevated rates of ion and acid-base regulation under environmental hypercapnia.