Environmental transitions leading to spatial physical-chemical gradients are of ecological and evolutionary interest because they are able to induce variations in phenotypic plasticity. Thus, the adaptive variability to low-pH river discharges may drive divergent stress responses [ingestion rates (IR) and expression of stress-related genes such as Heat shock protein 70 (Hsp70) and Ferritin] in the neritic copepod Acartia tonsa facing changes in the marine chemistry associated to ocean acidification (OA). These responses were tested in copepod populations inhabiting two environments with contrasting carbonate system parameters (an estuarine versus coastal area) in the Southern Pacific Ocean, and assessing an in situ and 96-h experimental incubation under conditions of high pressure of CO2 (PCO2 1200 ppm). Adaptive variability was a determining factor in driving variability of copepods' responses. Thus, the food-rich but colder and corrosive estuary induced a traits trade-off expressed as depressed IR under in situ conditions. However, this experience allowed these copepods to tolerate further exposure to high PCO2 levels better, as their IRs were on average 43% higher than those of the coastal individuals. Indeed, expression of both the Hsp70 and Ferritin genes in coastal copepods was significantly higher after acclimation to high PCO2 conditions. Along with other recent evidence, our findings confirm that adaptation to local fluctuations in seawater pH seems to play a significant role in the response of planktonic populations to OA-associated conditions. Facing the environmental threat represented by the inter-play between multiple drivers of climate change, this biological feature should be examined in detail as a potential tool for risk mitigation policies in coastal management arrangements.