The wind anomalies are a manifestation of an atmospheric counterpart to the oceanic El Niño. At the turn of the century, the British climatologist Gilbert Walker set out to determine the connections between the Malaysian-Australian monsoon and other climatic fluctuations around the globe in an effort to predict unusual monsoon years that bring drought and famine to the Asian sector. Unaware of any connection to El Niño, he discovered a coherent interannual fluctuation of atmospheric pressure over the tropical Indo-Pacific region, which he termed the Southern Oscillation (SO). During years of reduced rainfall over northern Australia and Indonesia, the pressure in that region (e.g., at what are now Darwin and Jakarta) was anomalously high and wind patterns were altered. Simultaneously, in the eastern South Pacific pressures were unusually low, negatively correlated with those at Darwin and Jakarta. A Southern Oscillation Index (SOI), based on pressure differences between the two regions (east minus west), showed low, negative values at such times, which were termed the “low phase” of the SO. During more normal “high-phase” years, the pressures were low over Indonesia and high in the eastern Pacific, with high, positive values of the SOI. In papers published during the 1920s and ’30s, Walker gave statistical evidence for widespread climatic anomalies around the globe being associated with the SO pressure “seesaw.”

In the 1950s, years after Walker’s investigations, it was noted that the low-phase years of the SOI corresponded with periods of high ocean temperatures along the Peruvian coast, but no physical connection between the SO and El Niño was recognized until Norwegian American meteorologist Jacob Bjerknes, in the early 1960s, tried to understand the large geographic scale of the anomalies observed during the 1957–58 El Niño event. Bjerknes formulated the first conceptual model of the large-scale ocean-atmosphere interactions that occur during El Niño episodes. His model has been refined through intensive research since the early 1970s.

During a year or two prior to an El Niño event (high-phase years of the SO), the westward trade winds typically blow more intensely along the Equator in the equatorial Pacific, causing warm upper-ocean water to accumulate in a thickened surface layer in the western Pacific where sea level rises. Meanwhile, the stronger, upwelling-favourable winds in the eastern Pacific induce colder surface water and lowered sea levels off South America. Toward the end of the year preceding an El Niño, the area of intense tropical storm activity over Indonesia migrates eastward toward the equatorial Pacific west of the International Date Line (which corresponds in general to the 180th meridian of longitude), bringing episodes of eastward wind reversals to that region of the ocean. These wind bursts excite extremely long ocean waves, known as Kelvin waves (imperceptible to an observer), that propagate eastward toward the coast of South America, where they cause the upper ocean layer of relatively warm water to thicken and sea level to rise.

The tropical storms of the western Pacific also occur in other years, though less frequently, and produce similar Kelvin waves, but an El Niño event does not result, and the waves continue poleward along the coast toward Chile and California, detectable only in tide-gauge measurements. Something else occurs prior to an El Niño that is not fully understood: as the Kelvin waves travel eastward along the Equator, an anomalous eastward current carries warm western Pacific water farther east, and the warm surface layer deepens in the central equatorial Pacific (east of the International Date Line). Additional surface warming takes place as the upwelling-favourable winds bring warmer subsurface water to the surface. (The subsurface water is warmer now, rather than cooler, because the overlying layer of warmer water is now significantly deeper than before.) The anomalous warming creates conditions favourable for the further migration of the tropical storm centre toward the east, giving renewed vigour to eastward winds, more Kelvin waves, and additional warming. Each increment of anomalies in one medium (e.g., the ocean) induces further anomalies in the other (the atmosphere) and vice versa, giving rise to an unstable growth of anomalies through a process of positive feedbacks. During this time the SO is found in its low phase.

After several months of these unstable ocean-atmosphere interactions, the entire equatorial zone becomes considerably warmer (2–5 °C [3.6–9 °F]) than normal, and a sizable volume of warm upper ocean water is transported from the western to the eastern Pacific. As a result, sea levels fall by 10–20 cm (about 4–8 inches) in the west and rise by larger amounts off the coast of South America, where sea surface temperature anomalies may vary from 2–8 °C above normal. Anomalous conditions typically persist for 10–14 months before returning to normal. The warming off South America occurs even though the upwelling-favourable winds there continue unabated: the upwelled water is warmer now, rather than cooler as before, and its associated nutrients are less plentiful, thereby failing to sustain the marine ecosystem at its prior productive levels.

The current focus of oceanographic research is on understanding the circumstances leading to the demise of the El Niño event and the onset of another such event several years later. The most widely held hypothesis is that a second class of long equatorial ocean waves—Rossby waves with a shallow surface layer—is generated by El Niño and that they propagate westward to the landmasses of Asia. There the Rossby waves reflect off the Asian coast eastward along the Equator in the form of upwelling Kelvin waves, resulting in a thinning of the upper ocean warm layer and a cooling of the upper ocean as the winds mix deeper, cooler water to the surface. This process is thought to initiate one to two years of colder-than-average conditions until westward-propagating Rossby waves are again generated, functioning as a switching mechanism, this time to start another El Niño sequence.

Another goal of scientists is to understand climate change on the scale of centuries or longer and to make projections about the changes that will occur within the next few generations. Yet, determinations of current climatic trends from recent data are made difficult by natural variability at shorter timescales, such as the El Niño phenomenon. Many scientists are attempting to understand the mechanisms of change during an El Niño event from improved global measurements so as to determine how the ocean-atmosphere engine operates at longer timescales. Others are studying prehistoric records preserved in trees, sediments, and fossil corals in an effort to reconstruct past variations, including those like El Niño. Their aim is to remove such short-term variations so as to be able to make more accurate estimates of long-term trends.