Exposure of the toxigenic dinoflagellate <em>Alexandrium catenella</em> to variations in <em>p</em>CO<sub>2</sub>/pH, comparable to current and near-future levels observed in Southern Chilean fjords, revealed potential functional adaptation mechanisms. Under calculated conditions for pH<sub>(total scale)</sub> and <em>p</em>CO<sub>2</sub> 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 <em>p</em>CO<sub>2</sub>/pH conditions (∼8.1). DistaLM analysis between physiological relevant carbonate system parameters (CO<sub>2</sub>, HCO 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 <em>p</em>CO<sub>2</sub> conditions. Light intensity as co-factor during experiments (50 vs. 100 μmol photons m<sup>−2</sup> s<sup>−1</sup>) 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 <em>p</em>CO<sub>2</sub>. We suggest that <em>A. catenella</em> Chilean strains are highly adapted to spatio-temporal <em>p</em>CO<sub>2</sub>/pH fluctuations in Chilean fjords, becoming a resilient winner from expected climate change effects.