AbstractOngoing ocean deoxygenation is threatening marine organisms globally. In eastern boundary upwelling systems, planktonic copepods dominate the epipelagic zooplankton, being crucial in the marine food web. Yet, they must cope with severe hypoxia caused by shoaling of the oxygen minimum zone. Based on laboratory experiments during 2021, we found differential responses in the metabolic rate (MR) and critical oxygen partial pressure of three abundant copepods. Calanoides patagoniensis doubled its MR during the upwelling season, so better exploiting the spring phytoplankton bloom for feeding and reproduction while maintaining their critical oxygen partial pressure unchanged between seasons. Contrastingly, Paracalanus cf. indicus and Acartia tonsa, maintained their MRs throughout seasons, but significantly increased their critical oxygen partial pressure during the upwelling period, becoming less tolerant to hypoxia. Field observations showed that oxygen levels equal to or lower than the critical oxygen partial pressure is a common condition (70% of occurrence) that copepods encounter during the year in the upper 50 m layer. These findings suggest a species‐dependent trade‐off between the MR and the critical oxygen partial pressure, where some species can maintain the latter despite fluctuations in their MR (improved hypoxia tolerance) or maintain their MR at the expenses of a larger critical oxygen partial pressure (improved energy expenditures). These adaptive responses, under oxygen levels equal to or lower than the critical oxygen partial pressure, suggest that exacerbated hypoxia, driven by ocean deoxygenation and increased upwelling, will alter copepod distribution and cause higher copepod mortality, with potentially drastic consequences for marine food webs.