The good news is, there is no bad time to go to Galapagos! However, there are a few factors to keep in mind as you are making your travel plans.
From June-November, the Humboldt Current brings colder, nutrient-rich water through the archipelago which also affects the land temperature. Air and water temperature this time of year average about 72° F/22°C, and you might experience “Garua” or misty rain occasionally.
The advantage for wildlife-seeking travelers is that the food-filled current attracts fish and marine birds like albatross and penguins, making them more plentiful. Those seeking a scuba experience might prefer this time of year for more abundant marine life.
Conversely, December-May brings a little warmer water (average 76°F/25°C) and air (average 80°F/27°C), as well as humidity. Seas are calmer, and rainfall is common for short periods only. This is a good time to see Marine Iguanas, Flightless Cormorants and Sea Turtles nesting, and Blue Footed Boobies in courtship.
The busiest season for tourists in Galapagos is from mid-June to mid-September, and mid-December to mid-January. If you think you’d like to come to Galapagos during those months it’s a good idea to plan several months ahead.