The acid-base status and balance of molluscs are considered to be susceptible to environmental changes, especially in the context of ocean acidification (OA). Here, we studied the effects of manipulated seawater carbonate chemistry on the acid-base status of scallop Chlamys farreri and abalone Haliotis discus hannai. The haemolymph pH of the tested individuals showed a fast response to acidified seawater incubation, and the pH level was restored to a normal value within 1 h of recovery in control seawater. However, no significant correlation (P > 0.05) was found between haemolymph pH and seawater pCO2 or pH, while the squared Pearson correlation coefficient (R2) ranged from close to zero to 0.41. In addition, although the pCO2 level of total alkalinity (TA)-lowered seawater was lower than half of that in the control, molluscs eliminated less CO2 (less than 80%) to TA lowered waters than to the control waters. These findings seem to disagree with the crucial role of seawater pCO2 in influencing the acid-base balance of molluscs. CO2 elimination occurs in the microenvironment, and CO2 first diffuses to limited amounts of seawater that tightly surround the gills, causing dissolved inorganic carbon (DIC) accumulation in the ventilation sites, which leads to a sharp increase in the pCO2 of the surrounding seawater. Moreover, in this microenvironment, the pCO2 level increases much faster and more greatly if the environmental seawater is acidified or contains a lower level of TA. Therefore, mollusc acid-base status is influenced by rapidly varying pCO2 levels at the ventilation site, which is largely independent of that of the rest of the incubating seawater. In summary, CO2 elimination by molluscs relies heavily on the carbonate chemistry of environmental seawater, and seawater buffering capacity should be taken into consideration instead of considering only pCO2 or pH in studying the acid-base balance of marine molluscs.