The Galapagos archipelago, rising from the eastern equatorial Pacific Ocean some 900 km off the South American mainland, hosts an iconic and globally significant biological hotspot. The islands are renowned for their unique wealth of endemic species, which inspired Charles Darwin's theory of evolution and today underpins one of the largest UNESCO World Heritage Sites and Marine Reserves on Earth. The regional ecosystem is sustained by strongly seasonal oceanic upwelling events-upward surges of cool, nutrient-rich deep waters that fuel the growth of the phytoplankton upon which the entire ecosystem thrives. Yet despite its critical life-supporting role, the upwelling's controlling factors remain undetermined. Here, we use a realistic model of the regional ocean circulation to show that the intensity of upwelling is governed by local northward winds, which generate vigorous submesoscale circulations at upper-ocean fronts to the west of the islands. These submesoscale flows drive upwelling of interior waters into the surface mixed layer. Our findings thus demonstrate that Galapagos upwelling is controlled by highly localized atmosphere-ocean interactions, and call for a focus on these processes in assessing and mitigating the regional ecosystem's vulnerability to 21st-century climate change.