Paleoclimate reconstructions of El Niño/Southern Oscillation (ENSO) behavior often rely on oxygen isotopic records from tropical corals (δ18O). However, few reef‐based observations of physical conditions during El Niño events exist, limiting our ability to interpret coral δ18O. Here we present physical and geochemical measurements from Palmyra Atoll (5.9°N, 162.1°W) from 2014–2017, along with a data assimilation product using the isotope‐enabled Regional Ocean Modeling System (isoROMS). Coral δ18O signals are comparably strong in 2014–2015 and 2015–2016; notably, over 50% of the signal is driven by seawater δ18O, not temperature. If a constant seawater δ18O:salinity relationship were present, this would imply a comparable salinity anomaly during both events. However, salinity changes are much larger during 2014–2015, indicating a highly nonstationary relationship. isoROMS then shows that advection strongly influences δ18O during both the 2014–2015 and 2015–2016 El Niño, driving differences in the salinity/seawater δ18O relationship. This demonstrates the need for considering ocean dynamics when interpreting coral δ18O.