The coastal ecosystems and the civilizations that flourished on the Peruvian coast have been shaped by Pacific currents. The Peruvian or Humboldt Current flowing northward along the coast of South America, carrying cold, nutrient-rich water from the ocean around Antarctica almost to the Equator, where it veers eastward toward the Galapagos Islands. An upwelling off the coast of Peru brings this layer of water to the surface, providing nutrients for an abundance of plankton that provide food for a large number of fish, especially anchovies and sardines. This marine ecosystem also includes sea birds, dolphins, porpoises, sea lions and fur seals that feed on the fish. Many sea birds nest on rocky capes and islands where guano collects.

Periodically, the current patterns on the coast change. The trade winds, which usually blow east to west, die down and the cold layer of water sinks. A surface wave, called a Kelvin wave, moves from west to east across the Pacific Ocean toward the South American coast. Without the upwelling of cold, nutrient-rich water, fish are less plentiful, and populations of sea birds and marine mammals may migrate away or simply collapse. Fishermen who noticed this phenomenon around Christmas time called it El Niño, "the little boy," for the Christ child. The combined effect of changes in ocean currents and winds is known as the El Niño-Southern Oscillation, or ENSO. It often causes heavy rains on the usually arid coast, and may cause heavy rain or drought in the Andes.

El Niño is usually associated with disaster, but that is mainly because the population in areas prone to flash flooding has increased in recent decades. The dry forest and other coastal ecosystems flourish with the precipitation. Early coastal civilizations could have benefited from the precipitation, but the rains could also damage or destroy their adobe dwellings and temples. Recent studies indicate that human activities might have magnified El Niño's negative effects. A collapse of the Nazca culture, on the south-central coast, around 500 AD apparently coincided with heavy rains from El Niño. Pollen studies show that the forest in the area had been cleared for agriculture, which might have left the population unprotected against heavy flooding.