With an emerging El Niño signal raising the likelihood of marine heatwaves and coral bleaching on the Great Barrier Reef in 2026/27, anticipating impacts on reef fish populations requires empirical benchmarks from past events. The 2016 GBR mass bleaching — one of the most intensively documented thermal extremes in Australian waters — provides exactly that. Here we report on integrated physiological responses in nine common reef fish species (Pomacentridae and Apogonidae) sampled from reefs around Lizard Island across four time points: prior to thermal stress, early warming, peak temperatures, and post-heatwave recovery. Building on our published transcriptomic analyses that revealed species-specific yet functionally overlapping molecular stress responses, we tested whether these shifts were reflected in whole-animal physiology. Peak warming was associated with altered body condition, reduced gut fullness, remodelling of gill morphology, and restructured metabolic enzyme activities in gill and muscle tissue — collectively indicating reorganisation of both aerobic and anaerobic capacity under sustained thermal stress. Critically, several physiological metrics showed incomplete recovery once temperatures declined, suggesting that the energetic costs of acute plasticity extend well beyond the heatwave itself, with potential carry-over consequences for growth, reproduction, and survival. These findings provide concrete physiological benchmarks for predicting what another severe bleaching event would mean for wild reef fish communities. They also make the case for integrating targeted physiological monitoring — across species, before, during, and after thermal events — into heatwave preparedness and rapid-response frameworks for the GBR.