The recently released NCEP Climate Forecast System Reanalysis (CFSR) is used to examine the response to ENSO in the northeast tropical Pacific Ocean (NETP) during 1979–2009. The normally cool Pacific sea surface temperatures (SSTs) associated with wind jets through the gaps in the Central American mountains at Tehuantepec, Papagayo, and Panama are substantially warmer (colder) than the surrounding ocean during El Niño (La Niña) events. Ocean dynamics generate the ENSO-related SST anomalies in the gap wind regions as the surface fluxes damp the SSTs anomalies, while the Ekman heat transport is generally in quadrature with the anomalies. The ENSO-driven warming is associated with large-scale deepening of the thermocline; with the cold thermocline water at greater depths during El Niño in the NETP, it is less likely to be vertically mixed to the surface, particularly in the gap wind regions where the thermocline is normally very close to the surface. The thermocline deepening is enhanced to the south of the Costa Rica Dome in the Papagayo region, which contributes to the local ENSO-driven SST anomalies. The NETP thermocline changes are due to coastal Kelvin waves that initiate westward-propagating Rossby waves, and possibly ocean eddies, rather than by local Ekman pumping. These findings were confirmed with regional ocean model experiments: only integrations that included interannually varying ocean boundary conditions were able to simulate the thermocline deepening and localized warming in the NETP during El Niño events; the simulation with variable surface fluxes, but boundary conditions that repeated the seasonal cycle, did not.