La Niña episodes also feature large-scale changes in the atmospheric winds across the tropical Pacific, including increased easterly (east- to- west) winds across the eastern Pacific in the lower atmosphere, and increased westerly (west-to-east) winds over the eastern tropical Pacific in the upper atmosphere. These conditions reflect an enhanced strength of the equatorial Walker Circulation.

During the developing phase of La Niña, the subsurface ocean structure is characterized by an abnormally shallow layer of warm water across the eastern tropical Pacific, in association with a reduced depth of the oceanic thermocline. Thus, the slope of the thermocline is increased across the basin. In very strong La Niña episodes, the thermocline can actually come very close to the ocean surface for extended periods. This cooling represents a decreased depth of the oceanic mixed layer, and accompanies the appearance of nutrient-rich waters very close to the ocean surface. Thus, its existence is quite beneficial to marine life throughout the region. Accompanying these conditions, the sea level height is lower than normal over the eastern Pacific, resulting in an increased slope of the ocean surface across the basin. There is also considerable evolution in the subsurface temperature and thermocline structure during both El Niño and La Niña episodes.