Abstract Sea‐level rise (SLR) alters nearshore hydrodynamics, yet its influence on coral reef thermal regimes under climate‐driven ocean warming remains poorly quantified. Using a fully coupled hydrodynamic–wave model validated at Palmyra Atoll, we isolate how SLR modifies temperature variability during a projected 2050 marine heatwave. Results show that while basin‐scale warming raises reef bottom temperatures broadly, SLR deepens shallow habitats and enhances tidal exchange, reducing daily and maximum temperatures by more than 0.5°C across 16% of reef area. Heat budget analysis reveals that SLR shifts the balance between advective and surface flux terms, damping thermal extremes through increased water volume and flow. These results identify physical feedback between SLR and ocean warming that modulates heat accumulation in shallow tropical systems, providing a mechanism for localized thermal buffering amid global ocean warming.