Exposure of the toxigenic dinoflagellate Alexandrium catenella to variations in pCO2/pH, comparable to current and near-future levels observed in Southern Chilean fjords, revealed potential functional adaptation mechanisms. Under calculated conditions for pH(total scale) and pCO2 ranging from 7.73-8.66 to 69.7-721.3 μatm, respectively, the Chilean strain Q09 presented an optimum growth rate and dissolved inorganic carbon (DIC) uptake at near-equilibrium pCO2/pH conditions (˜8.1). DistaLM analysis between physiological relevant carbonate system parameters (CO2, Symbol, and H+) and cellular rates (growth rate and DIC uptake) identified Symbol as the unique variable explaining a significant portion of the physiological response. Estimations of equivalent spherical diameter (ESD) and chain-formation index (CI) revealed reduced cell size and enhanced chain formation at high pH/low pCO2 conditions. Light intensity as co-factor during experiments (50 vs. 100 μmol photons m−2 s−1) produced no effect on ESD and CI. Cells exposed to low light; however, had reduced cell growth and DIC uptake especially at high pH/low pCO2. We suggest that A. catenella Chilean strains are highly adapted to spatio-temporal pCO2/pH fluctuations in Chilean fjords, becoming a resilient winner from expected climate change effects.