To comprehend El Niño, you need to understand the interactions between the ocean and the atmosphere. Warm ocean surface water heats and adds moisture to the air above it, forming low pressure systems (Low). Cold surface water cools the air above it, forming high pressure systems (High). In a Low, the warm, moist air produces tropical thunderstorms. In a High, cool, dry air sinks back to the surface and there is no precipitation. Together, the High and Low create a circulation pattern in which surface winds blow toward the Low and upper-level winds blow toward the High.

Motion within the ocean is also important. Within the ocean, an invisible boundary called the thermocline separates warm surface water from cold, deeper water. A shallow thermocline indicates a small amount of warm water, and a deep thermocline means there's a lot of warm water. Because warm water takes up more space than cold water, average sea level is higher where the thermocline is deep and lower where the thermocline is shallow.

Meteorologists now recognize a phenomenon related to El Niño called La Niña, in which conditions are nearly opposite those of El Niño. The diagrams and text below compare the features of the ocean and atmosphere that accompany normal, El Niño, and La Niña conditions.