The following is from Emma Ridley, Expedition Leader with Lindblad Expeditions.
Living here year-round, one sees the complete transformation of life. I am often asked what the best time to visit the islands is, and my answer, invariably, is that every time is a good time as far as the wildlife goes. I recommend you make your decision based on your personal preferences.
The Galapagos is at the heart of a complex system of marine currents. From June to October, the cool Humboldt Current and cold upwellings of the equatorial undercurrent are at their peak, and the shores are bathed by cool waters. This creates surprisingly dry and cool conditions for the tropics, which is why the islands are mostly covered with desert ecosystems that include the magnificent forests of giant prickly-pear cactus trees and silvery incense trees.
The skies tend to be overcast and temperatures are extremely pleasant (70s to 80s F) and, although waters are cool (69-73 F), our wetsuits help you to enjoy the underwater just the same! This is definitely the right time if you are intolerant of hot, humid tropical conditions.
These cool waters bring abundant nutrients. The animals whose livelihoods depend on the ocean start gathering in their colonies and courting to find mates, so that once they have their offspring the surrounding waters will be filled with bountiful food. These include blue-footed boobies, waved albatross (May to January), sea lions, marine iguanas and more.
From January to April, water temperatures rise significantly (79-83 F) and the weather changes. It becomes hot (80s-low 90s F), with mostly blue skies and occasional showers. The arid ecosystems transform into lush, green ecosystems. The animals dependent on terrestrial food sources court and breed, including Darwin finches, giant Galapagos tortoises and land iguanas. This is also the nesting season of the green sea turtle. So take your pick, Galapagos is always in her prime.