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Abstract The impacts of El Niño‐Southern Oscillation (ENSO) on salinity and alkalinity in an equatorial coral reef lagoon (Kanton) are investigated using water samples collected in three non‐El Niño years (1973, 2012, and 2018) and one El Niño year (2015). A one‐dimensional, advective‐diffusive model is developed to aid in the interpretation of the sparse observations and make estimates of net ecosystem calcification (NEC) rates. The Kanton lagoon experiences extreme salinity and alkalinity variations driven by ENSO variations in precipitation. During the non‐El Niño years, salinity increases from the ocean (35.5 psu) to the back of the lagoon (38 psu) because evaporation exceeds precipitation, and water resides in the back of the lagoon for ∼180 days. Early in the 2015–2016 El Niño, the back of the lagoon is only ∼1 psu saltier than the ocean because precipitation had begun to exceed evaporation. The model suggests that during El Niño events, when precipitation substantially exceeds evaporation, the back of the lagoon is less salty than the ocean (30–32 psu). Alkalinity variations in the lagoon are primarily due to dilution or concentration driven by the ENSO variations in precipitation and NEC that causes an alkalinity deficit of ∼250 μmol/kg in the back of the lagoon. The estimated NEC rate in 2015 is ∼25% lower (4.1 mmol/day) than in the non‐El Niño years (5.3–5. 7 mmol/day). The NEC rates and coral cover measurements indicate that the Kanton lagoon has recovered from the complete loss of coral cover during the 2002–2003 El Niño. 

Marine heatwaves are triggering coral bleaching events and devastating coral populations globally, highlighting the need to identify processes promoting coral survival. Here, we show that acceleration of a major ocean current and shallowing of the surface mixed layer enhanced localized upwelling on a central Pacific coral reef during the three strongest El Niño–associated marine heatwaves of the past half century. These conditions mitigated regional declines in primary production and bolstered local supply of nutritional resources to corals during a bleaching event. The reefs subsequently suffered limited post-bleaching coral mortality. Our results reveal how large-scale ocean-climate interactions affect reef ecosystems thousands of kilometers away and provide a valuable framework for identifying reefs that may benefit from such biophysical linkages during future bleaching events. 

Abstract Ocean warming is killing corals, but heat-tolerant populations exist; if protected, they could replenish affected reefs naturally or through restoration. Palau’s Rock Islands experience consistently higher temperatures and extreme heatwaves, yet their diverse coral communities bleach less than those on Palau’s cooler outer reefs. Here, we combined genetic analyses, bleaching histories and growth rates of Porites cf. lobata colonies to identify thermally tolerant genotypes, map their distribution, and investigate potential growth trade-offs. We identified four genetic lineages of P . cf. lobata . On Palau’s outer reefs, a thermally sensitive lineage dominates. The Rock Islands harbor two lineages with enhanced thermal tolerance; one of which shows no consistent growth trade-off and also occurs on several outer reefs. This suggests that the Rock Islands provide naturally tolerant larvae to neighboring areas. Finding and protecting such sources of thermally-tolerant corals is key to reef survival under 21 st century climate change.