Located at the confluence of five ocean currents, the climate in the Galapagos Islands is different than one might imagine from islands located on the equator. The climate is dominated by the prevailing current; which creates strong, unpredictable tides between islands, cooler than normal temperatures, and ultimately results in the unique ecology of the islands.

The main ocean currents effecting the Galapagos Islands are the cold Counter Equatorial (Cromwell) Current from the west, the cold Humboldt (Peruvian Oceanic and Peruvian Coastal) Current and the from the southeast, the South Equatorial Current from the east, and the warm North Equatorial (Panama) Counter Current from the northeast which brings with it the devastating and infrequent El Niño Current. The mix of these currents and the location of the island in relation to the mix cause a wide variation of water temperatures from month to month and island to island.

Predominating the Galapagos climate during the summer and fall the nutrient rich Humboldt Current runs up the west coast of South America from Antarctica.  This strong current brought both penguins and fur seals to the Galapagos.  

As the Humboldt Current moves through the islands it cools both the land and sea temperatures bringing with it a subtropical climate. Winds come from the southeast creating an inversion layer. Low straight formed clouds cover the islands much of the day. A light mist known as locally as ‘garúa’ frequents the highlands and at times sweeps down to the shore. Though there is more precipitation this time of year it is referred to as the "dry season" since the mist-like garaua made it difficult for settlers to collect water. 

The Humboldt Current is strongest in September, causing the surface waters to be choppy.  This is the time when most of the boats cruising the islands go into dry-dock. These later months are a good time for Green Sea Turtle sightings (during their mating season) and shark sightings are still high, but rays are seen less frequently.

In November as the Humboldt Current leaves the Galapagos and the warm waters from the Panama Current return to dominate the climate thru May.  The inversion layer leaves the Galapagos.  During these months the water temperatures rise to 70º to 80º F (21º-27º C). The skies are generally clear with the exception of occasional short-strong rains from which settlers we able to catch water, giving this season the name the "wet season".

The waters of the Panama Current have far less nutrients than the Humboldt Current and offer the best visibility underwater for diving and snorkeling.   

Every 2 to 7 years the strong westward-blowing trade winds subside. These winds, which normally pull the warm waters to the west and allow the nutrient rich Humboldt Current to reach the Galapagos, fail to leave the islands. Instead the warm water slowly moves back eastward across the Pacific. The food chain is broken and the breeding cycle of many of the animals including;

Galapagos Penguins and Marine Iguanas, which feed off the upwelling is interrupted. Warmer water temperatures also cause an increase in the mortality rate of the young birds and animals. Plants, on the other hand, seem to thrive during El Niño years. Plants, which may not have flowered in years, will flower again due to the excess water.

Peruvians named this phenomenon El Niño, for the Christ child, because it first appears around Christmas. Major El Niño Currents occurred as recently as 1982 and 1998.