The early stages of intertidal mussels, including the green-lipped mussel, Perna canaliculus, face both direct and indirect environmental threats. Stressors may influence physiological status and, ultimately, survival. An understanding of the nature of stress experienced is critical to inform conservation and aquaculture efforts. Here, we investigated oxidative stress dynamics in juvenile P. canaliculus in relation to emersion duration (1–20 h) and relative humidity (RH, 29–98%) by quantifying oxidative damage (protein carbonyls, lipid hydroperoxides, 8-hydroxydeoxyguanosine) and enzymatic antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reductase). Mussels held in low RH during emersion experienced severe water loss (>70%), high mortality (>80%) and increased oxidative damage (35–45% increase compared to control conditions), while mussels held at high RH were not impacted, even after 20 h of air exposure. Following re-immersion, reoxygenation stress resulted in further increases in damage markers in mussels that had experienced dryer emersion conditions; protective action of antioxidants increased steadily during the 10 h re-immersion period, apparently supporting a reduction in damage markers after 1–5 h of immersion. Clearly, conditions during emersion, as well as duration, substantially influence physiological performance and recovery of juvenile mussels. Successful recruitment to intertidal beds or survival in commercial aquaculture operations may be mediated by the nature of emersion stress experienced by these vulnerable juveniles.