Abstract Coral reefs in the northern South China Sea experience some of the world’s most energetic internal waves (IWs), yet records of how these dynamics influence reef‐level conditions are rare. Using over 6 years of temperature data from Dongsha Atoll, we show that IWs drive diel temperature fluctuations that reduce subsurface heat exposure and entrain cool, nitrate‐rich water onto the reef slope. This internal‐wave‐driven upwelling is strongly modulated by mesoscale circulation: positive sea‐level anomalies associated with Kuroshio intrusion and long‐lived anticyclonic eddies cause a two‐stage suppression of internal‐wave generation and arrival, first near the Luzon Strait and subsequently over the reef. Reduced reef‐slope internal‐wave expression lowered nitrate exposure by >100‐fold at the reef. Typhoons injected near‐inertial energy but were followed by declines in cooling and nitrate supply until restratification. These results demonstrate mesoscale and episodic processes regulating internal‐wave cooling and nutrient upwelling, revealing coupled, multi‐scale physical‐biogeochemical controls on reef resilience under ocean warming.