Weather changes as altitude increases in the large islands. Temperature decreases gradually with altitude, while precipitation increases due to the condensation of moisture in clouds on the slopes. There is a large variation in precipitation from one place to another, not only with altitude but also depending on the location of the islands, and also with the seasons.The following table corresponding to the wet 1969 shows the variation of precipitation in different places of Santa Cruz Island. The precipitation also depends on the geographical location. During March 1969 the precipitation over Charles Darwin Station, on the southern coast of Santa Cruz was 249.0 mm, while on Baltra Island the precipitation during the same month was only 137.6 mm. This is due to the fact that Baltra is located behind Santa Cruz with respect to the prevailing southerly winds, so most of the moisture gets precipitated in the Santa Cruz highlands.There are significant changes in precipitation from one year to another too. At Charles Darwin Station the precipitation during March 1969 was 249.0 mm, but during March 1970 it was only 1.2 mm

July to November, the temperatures are a bit cooler and range 60-75°F (18-24°C), with water temperatures of 70°F (21°C). July through November is the garua season. Garua is a mist that forms in the highlands, providing moisture. The air temperature can be slightly lower, but the equator is still a warm place to visit. During this time of year a cold ocean current from the south, called the Antarctic Humboldt current, causes the water temperature to drop slightly.

Garua is Spanish for mist, and is also used to describe the weather conditions that persist for several months of the year in the Galapagos. The garua results when warm air masses move over the cool Humboldt Current, causing moisture to condense out of the atmosphere. During El Niño years, the garua is replaced by heavy rainfall. Even during the warmth of day, the mist persists at high elevations, although lower elevations may be dry. In this image, the top half of the picture comprises the cloud-like mist, which condenses on the green vegetation (foreground), whereas lower down toward the ocean (middle right), the air is clear.

The origins of the Galapagos Islands are best understood in a geological context. The theory of plate tectonics that underpins modern geology offers a neat hypothesis for the presence of the Galapagos. Unlike continents, which are large masses of granitic rock surrounded by basaltic oceanic plates, the Galapagos Islands, which is an island chain in the middle of the ocean are comprised mostly of basalt, is the result of eruptions from oceanic plates. To explain this, geologists devised the "hotspot" model. This is based on the idea that a plume of hot material is rising from deep in the earth's mantle and melts the overlying oceanic plate. This material rises to the surface and solidifies into the islands we see today. There is good circumstantial evidence for this idea, but the origin of the underlying mechanism within the mantle remains mysterious.