The Galapagos weather despite their tropical location is not so warm because the islands are surrounded by relatively cold waters brought northwards by the Humboldt Current. The Galapagos Islands has two main seasons, each of which has an effect on the flora and fauna: the warm and wet season from January to June and the cool and dry (garua) season, from July to December. During the "garua" season, cooler waters from the Humboldt Current are driven to the Galapagos by the southeast trade winds, with an average sea temperature of 22°C (71°F).

As a result, there is warm tropical air passing over cool water. The moisture evaporating from the sea is concentrated in an inversion layer (300 to 600 m above sea level) and the higher parts of the islands, which intercept this layer, receive precipitation in the form of garua (mist rain). While lowland areas remain dry though cool.

During the warm season the southeast trade winds diminish in strength and warmer waters from the Panama Basin flow through the islands. The average sea temperature rises to 25° C (77°F). Warmer waters cause the cool season inversion layer to break up, and the Galapagos Islands experience a more typical tropical climate with blue skies and occasionally heavy showers. In some years, the flow of warm water is much greater than normal, and an "El Niño" year results. Surface water temperatures are higher and rainfall can increase greatly. Life on land blossoms but seabirds and sea life, which depend on the more productive, cooler waters, may experience dramatic breeding failures.