Although located on the Equator, the Humboldt Current brings cold water to the islands, causing frequent drizzles during most of the year. The weather is periodically influenced by the El Niño events, which occur about every 3–7 years and are characterized by warm sea surface temperatures, a rise in sea level, greater wave action, and a depletion of nutrients in the water.
During the season known as the garua (June to November), the temperature by the sea is 22 °C (72 °F), a steady and cold wind blows from south and southeast, frequent drizzles (garuas) last most of the day, and dense fog conceals the islands. During the warm season (December to May), the average sea and air temperature rises to 25 °C (77 °F), there is no wind at all, there are sporadic, though strong, rains and the sun shines.
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 range 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:
|Location||Charles Darwin Station||Devine Farm||Media Luna|
|Altitude||6 m||320 m||620 m|
|January||23.0 mm||78.0 mm||172.6 mm|
|February||16.8 mm||155.2 mm||117.0 mm|
|March||249.0 mm||920.8 mm||666.7 mm|
|April||68.5 mm||79.5 mm||166.4 mm|
|May||31.4 mm||214.6 mm||309.8 mm|
|June||16.8 mm||147.3 mm||271.8 mm|
|July||12.0 mm||42.2 mm||135.6 mm|
|August||3.8 mm||13.7 mm||89.5 mm|
|September||18.5 mm||90.9 mm||282.6 mm|
|October||3.2 mm||22.6 mm||96.5 mm|
|November||11.0 mm||52.8 mm||172.7 mm|
|December||15.7 mm||84.1 mm||175.3 mm|
|TOTALS||469.7 mm||1901.7 mm||2656.4 mm|
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 (9.80 in), while on Baltra Island, the precipitation during the same month was only 137.6 mm (5.42 in). This is because 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 (9.80 in), but during March 1970, it was only 1.2 mm (0.05 in).