The Galapagos is by definition an equatorial destination. The equator cuts across the north end of Isabela and darts in between Santiago and Genovesa. So there is no “seasonal” variation in the traditional sense. But there are distinct seasons, for certain. These seasons, and their effects on the potential traveler, can be directly attributed to the three major currents that meet at the Galapagos. More specifically, whichever current is “winning” at a given time of year will directly affect the air temperature, the water temperatures and even the amount of moisture in a given time of year.
The Humboldt Current is a cold current that flows north out of the Southern Ocean, along the coast of Chile. It brings colder waters, colder air temperatures, stronger winds and generally rougher seas to the Galapagos, usually from July until October. But with these cold waters come superb amounts of nutrients, which supports the aquatic life in the area.
The Cromwell Current comes along the equator from west to east. One might expect this to mean it’s a warm current, but oddly enough, it too is a cold water current, as it is heaving up from the deepest parts of the Pacific, bringing lots of nutrients with it. The Cromwell Current very rarely overpowers the other two currents, but does generally keep the waters on the west side of Isabela several degrees colder, and therefore significantly clearer - a nice bonus for travelers hoping to enjoy some good snorkeling.
The Panama Current is a warm water current that flows south and west from Central America. This current tends to be strongest from January to May. Along with the warm water comes warmer air, filled with much more moisture. When the Panama Current is strong, the Galapagos is receiving more rain, and the ecosystem is “greening up”. Several species of both birds and reptiles take advantage of the warmer waters and the wetter conditions to do their breeding, birthing and child-rearing.
So, as you can see, there are different seasons, caused by the different currents. So which season is best for a visit? They are all good! Sure, July thru October has colder water temps (wetsuits are a good idea at this time), chillier air temps, and rougher waters. But the waters are a bit clearer because of that temperature, so the snorkeling is particularly good. Yes, January thru May has warmer air temps, warmer water temps, and calmer winds, not to mention the more active mating and rearing cycles of many animals, but there is a better chance of significant rain (at least on land, that is). Its enough of a toss-up that the real factors are much more societal. Most folks visit the Galapagos when it matches their vacation time (Christmas, Spring Breaks, Summer Vacations) or when it matches the best time to visit another destination nearby, such as Machu Picchu or the Amazon.