Coral reefs are extremely sensitive ecosystems to climate change and especially to the warming oceans. Since 1980, three massive El Niño-associated heat stress periods triggered widespread bleaching events in the tropical Pacific that sometimes led to coral mortality. The understanding of potentially mitigating phenomena is crucial to choose where to focus conservation efforts. Through its capacity to bring cool, nutrient-enriched water in the warm oligotrophic shallows, upwelling can provide heat shelters for nearshore ecosystems. Little is known about the dynamics of upwelling during El Niño in the central tropical Pacific. Using ten years of subsurface temperature data and a thermocline depth reanalysis product, we here study the interconnections between upwelling intensity, thermocline depth and El Niño eventsin the central tropical Pacific.Previous methods were designedto quantify upwelling dynamics, in terms of cold-waterintrusion in the warm shallows or cold pulses. However, these often lackthe ability to identify individual events, are parameter heavy, which means they require knowledge on the local hydrography, and are unable to differentiate the physical processes inducing the cooling event. Here, we first developeda new, automated and locally adapted detection method based on a temperature stratification index. Not only our algorithm solves issues encountered by the previous methods as it is automatically tuned to the local environment, it does not require any parameter, and it separates upwelling from other processes, but we show that it improves the detection rate by 10% compared to previously published methods.Using our newly developed method, we quantifiedupwelling dynamics in ten years of subsurface temperature at five locations in the U.S. unaffiliated territory of the Pacific Remote Island Area. We observed extreme upwelling eventsat all five locations, and we show that these events are feature of strong and very strong El Niño events and their following La Niña as (1) theyproducethermocline shoaling patterns and (2) shallow thermoclines are associated with intensified upwelling periods. Overall, our results show that El Niñoand La Niñacan producetemporary upwelling-exposed areas that act as shelters for nearshoreecosystems during intense heat stress. On the contrary, El Niño can also inhibit upwelling in previously exposed areas, temporary redistributing potential shelters. The understanding of the thermocline shoaling patternsduring El Niño could provide geographical locations that could be naturally protected during El Niño and are therefore worthy of conservation efforts.