Marine organisms are constantly exposed to stress, such as changes in seawater temperature, which may elicit biochemical, molecular, and physiological changes. In the present study, an integrative approach to evaluate stress in the green-lipped mussel Perna canaliculus exposed to control, moderate, and severe heat stress was used. Flow cytometry (FCM) was used to measure hemolymph parameters, including hemocyte concentration, viability, and reactive oxygen species (ROS) production. Spectrophotometry and a handheld electrochemical meter were used to determine the total antioxidant capacity (TAC) of hemolymph and gill tissue, and metabolomics was used to contrast specific metabolic responses among treatments. For hemolymph parameters measured using FCM, the number of nonviable hemocytes increased with the severity of heat shock. The proportion of superoxide-positive hemocytes mirrored the increase in nonviability; by contrast, the general ROS production initially increased following moderate heat shock, but then decreased after severe heat shock. Trolox-equivalent antioxidant capacity in the gill tissue and fast-acting antioxidant levels in the haemolymph showed small but significant decreases following heat shock, whereas the reciprocal pattern was seen for slow-acting and TAC in the hemolymph. Metabolomic profiles discriminated between treatments, with energy metabolism pathways appearing the most affected. The approach used in this study provides a deeper mechanistic understanding of the stress responses of organisms exposed to heat stress; however, these analytical techniques may be combined or used independently to measure stress in marine organisms in the laboratory or in the field, which can improve health assessments of wild and farmed aquatic organisms.