Do local conditions influence the capacity of organisms to cope with extreme heat? Over the summer of 2024, a heatwave swept through Okinawa’s reefs, causing extensive coral bleaching and putting reef residents under strain. Juveniles of the blue damselfish Chrysiptera cyanea, usually highly abundant during the summer reproduction season, became scarce. To investigate how heat stress affects transcriptional profiles in surviving juveniles - and whether local pollution induces compounded effects - we sampled fish across 6 coastal sites along a natural-urban gradient from May to August 2024, with water temperatures rising from 24 to >33°C. We found broadly parallel responses to increased temperatures across the sites, with thousands of dysregulated genes, and a decoupling between fish feeding status and appetite regulation – suggesting a disconnection between hormonal cues and organismal state. Site-specific effects on inflammation and immune response revealed complex interactions between urbanisation and regional heat stress. Together, our results point to extensive effects of heatwaves on the physiology and energetic balance in juvenile fish following reef settlement, potentially cascading to long-term consequences on survival and fitness.