Despite a very strong El Niño Southern Oscillation in 2015/2016, no coral mortality associated with bleaching was observed at the northern Galapagos (Ecuador) Islands of Darwin and Wolf. From March 2016 to March 2018, coral cover and health as well as water chemistry (NO3− and PO43−) and temperature were recorded. A marked heat anomaly reached 30 °C at Wolf in February 2016, but peak temperatures were attenuated after 2 d by a 4 °C drop. Temperature patterns at three depths (10, 15, and 20 m) and a subsequent and persistent phytoplankton bloom suggest topographically driven upwelling as the source of colder water and dissolved inorganic nutrients—both of which helped corals endure the heating episode. Consequently, no mortality and only partial bleaching were recorded in March 2016. Partially bleached corals contained numerous healthy zooxanthellae in deeper tissue layers. A continuous temperature record from 2012 to 2014 suggests that such upwelling events are common, inducing temperature fluctuations of up to 6 °C within 24 h during the observation period. Events at Wolf in 2016 suggest local upwelling reduced coral stress by relieving heat and by delivering nutrients required by corals to retain their regular temperature tolerance.