The major advantage of recirculating aquaculture systems (RAS) is the ability to manipulate and control environmental variables to optimize production efficiency. However, the characteristics of water recycling and high-density aquaculture in RAS may result in the rapid accumulation of carbon dioxide (CO2) when raising high-density marine fish. This study aimed to evaluate the effects of CO2 on growth-related parameters, tissue structure, acid-base homeostasis, and ion regulation in turbot (Scophthalmus maximus). Turbot were subjected to five different CO2 treatments (C, 8, 16, 24, and 32 mg/L) at a temperature of 14 °C for durations of 7, 15, 30, and 60 days. The results indicated a substantial reduction in specific growth rate with increasing duration of CO2 exposure, accompanied by a significant increase in feed conversion rate. Exposure to CO2 also triggered the deposition of lipids or glycogen in the turbot liver, inhibiting the expression of growth factors. Additionally, it caused dissolution of the intestinal lamina propria and vacuolation of the intestinal mucosa. Even exposure to low levels of CO2 (8 mg/L) caused damage to the turbot gill tissue. Plasma analysis of turbot showed significantly higher concentrations of plasma HCO3− and significantly lower concentrations of Na+ and Cl−. Plasma HCO3− concentrations reached a maximum of 33.35 ± 0.13 mmol/L in the 32 mg/L treatment, and genes related to osmoregulation and acid-base homeostasis in the gill (H+-ATPase, NBCI, CA, AE, NHE1, NHE2) were altered based on the duration of CO2 exposure. The kidney did not exhibit significant damage throughout the experiment, and genes related to renal osmoregulation and acid-base homeostasis (AE, NBCI, NHE3, CAII, CAIV) were significantly elevated with CO2 exposure compared to the control group. These findings indicate that prolonged exposure to CO2 has a severe impact on feeding, resulting in damage to the liver and intestinal tissues, stress within the fish body, and disrupted expression of key genes related to the growth hormone/insulin-like growth factor axis. The study highlights the significance of monitoring CO2 concentrations in RAS for optimal marine fish health, as even concentrations below the 8 mg/L threshold have an impact on turbot. The involvement of turbot kidneys strengthens their buffering capacity against CO2, but CO2 stress still affects the gut and growth axis due to ion exchange and the progression of the HCO3−buffering system, leading to growth inhibition. Overall, this study provides valuable insights into the effects of CO2 exposure on turbot aquaculture and underscores the importance of monitoring CO2 concentrations in RAS to ensure optimal health of marine fish.