Coral reef ecosystems are highly sensitive to thermal anomalies, making them vulnerable to ongoing global warming. Yet, a variety of cooling mechanisms, such as upwelling, offer some respite to certain reefs. The Farasan Banks in the southern Red Sea is home to hundreds of coral reefs covering 16,000 km and experiences among the highest water temperatures of any coral-reef region despite exposure to summertime upwelling. We deployed an array of temperature loggers on coral reefs in the Farasan Banks, enabling us to evaluate the skill of satellite-based sea surface temperature (SST) products for capturing patterns of upwelling. Additionally, we used remote sensing products to investigate the physical drivers of upwelling, and to better understand how upwelling modulates summertime heat stress on coral communities. Our results show that various satellite SST products underestimate reef-water temperatures but differ in their ability to capture the spatial and temporal dynamics of upwelling. Monsoon winds from June to September drive the upwelling in the southern Red Sea via Ekman transport of surface waters off the shelf, and this process is ultimately controlled by the southwest Indian monsoon in the Arabian Sea. Further, the timing of the cessation of monsoon winds regulates the maximum water temperatures that are reached in September and October. In addition to describing the patterns and mechanisms of upwelling, our study sheds light on the broad ecological implications of this upwelling system, including modulation of coral bleaching events and effects on biodiversity, sea turtle reproduction, fish pelagic larval duration, and planktivore populations.