That is a great question! It is a question that scientists are currently struggling to answer. We know some important pieces of what causes El Nino... It starts with an atmospheric change that decreases the winds that usually blow from East to West across the tropical Pacific. The first result of this is that a pool of warm water that is usually trapped in the western tropical Pacific "sloshes" across the Pacific (moving towards the East) and ends up creating a warm layer across a large area of the tropical Pacific. This warm water is what causes tropical fish to end up in higher latitudes than normal, and the fishermen in South America notice that they can't catch their usual fish. From there, the effects of El Nino spread around the world, causing strange weather patterns due to the altered atmospheric and oceanic state.

The problem is, we don't really understand why the atmosphere changes from its normal pattern to begin with! It is one of the great mysteries that people are studying right now about the ocean and atmosphere. You can find out more by going to

el nino story

Here is an additional answer from a marine scientist:

Normal weather pattern:
Normally, the equatorial Pacific has warm waters near Indonesia, and colder surface water near Peru. This heats and cools the atmosphere above it, causing warmed air to rise near Indonesia and cool air to sink off Peru. This sets up an east-west "Walker Circulation" in which air rises in the west, travels eastward, sinks in the east, and travels westward again. This wind pattern helps to carry more warm water to the west, maintaining the sea-surface temperature (SST) pattern. This is the non-El Nino state.

However, once every few years, the SST pattern collapses: the warm water at Indonesia travels across the Pacific as a "Kelvin wave", leaving the surface uniformly warm. This keeps cool, nutrient-rich water from rising to the surface off Peru. Also, without the "cold east, warm west" SST pattern, the Walker Circulation ceases or even reverses. It takes several years for the system to return to normal.