El Niño episodes feature large-scale changes in the atmospheric winds across the tropical Pacific, including reduced easterly (east- to- west) winds across the eastern Pacific in the lower atmosphere, and reduced westerly (west-to-east) winds over the eastern tropical Pacific in the upper atmosphere near the tropopause. These conditions reflect a reduced strength of the equatorial Walker Circulation, which in strong El Niño episodes can be completely absent.

During the developing phase of the El Niño, the subsurface ocean structure is characterized by an abnormally deep layer of warm water and an increased depth of the thermocline across the eastern tropical Pacific. Thus, the slope of the thermocline is reduced across the basin. In very strong El Niño episodes, the thermocline can actually become flat across the entire tropical Pacific for periods of several months. Accompanying these conditions, the sea level height is higher than normal over the eastern Pacific, resulting in a decreased slope of the ocean surface height across the basin.  There is also considerable evolution in the subsurface temperature and thermocline structure during both El Niño and La Niña episodes.