El Niño (the boy in Spanish) is part of a wider climate system called El Niño Southern Oscillation, in which the Pacific Ocean and the atmosphere above it influence each other. This interaction drives the warming and cooling of the equatorial Pacific, which in turn affects the weather elsewhere in the world.
The process starts with surface water, propelled westward across the ocean by trade winds and heated by the sun as it travels, running into the Philippines, the Malay Archipelago and New Guinea. Over the course of between two and seven years the pool of warm water thus created grows into something with an area of about 12 million sq km.
Balmy, humid air rises from the pool, cooling and shedding rain as it does so, as part of a phenomenon called the Walker Circulation (see figure). Some of this air travels west, where it irrigates Indonesia with its precipitation. Some travels east, discharging its load on the Pacific, and then sinks back to the surface near the coast of South America, replacing the air that has travelled west as the trade winds.
Below the surface things are happening, too. The movement of warm water towards the Pacific’s west draws cool water to the surface in its east. This process, known as upwelling, lifts nutrients from the dark ocean bed to sunlit levels where they can be absorbed by planktonic algae and thus support some of the world’s richest sources of wild protein, the Peruvian anchoveta and the Tuna fishery.
As the pool of warm water grows, the ocean’s surface rises. This means the western equatorial Pacific’s surface can be up to 30cm higher than that of its eastern counterpart. Take the trade winds away, though, and this mountain of water will collapse and start spreading east. That collapse and spread is the essence of El Niño.
To a large extent, the pooled warm waters of the Pacific west are the author of their own destruction. Once their surface temperature exceeds 26.5°C, cyclones can form. These sap the trade winds’ energy, and thus their ability to keep the raised pool intact. The result is that the whole system quickly fails, the warm water sloshes back towards South America, and the "El Niño" is born.
Higher-than-usual sea-surface temperatures across the central and eastern equatorial Pacific then slow the trade winds further, accelerating the pool’s demise. The upwelling stops, and the fishery disappears. The ascending air that starts the Walker circulation moves east, and no longer brings rain to Indonesia. And the knock-on effects of the Walker circulation’s easterly movement echo around the Earth, disturbing rainfall systems everywhere, in a pattern that usually peaks in December.
Source here