There is no bad time to visit the Galapagos Islands. There is always something interesting to see and the weather is usually great. Still, there are a few variables you may want to consider.
Weather
The Equator passes through the Islands, so it’s never frigid, but there are significant seasonal variations. From June to December, currents bring cool water and air to the Islands. The islands are cooler, there is often rain or mist (garúa) and water temperatures are cool enough that you may want a wetsuit while snorkeling. From January to May, the Islands get hotter (sometimes it’s quite brutal) and there is less rain.
Wildlife
There are cycles and patterns to the wildlife as well, and you should bear this in mind if seeing a particular type of animal or behavior is important to you. For example, the tortoises migrate into and out of the highlands: if you want to see them in their natural habitat, best go between January and June. If you want to see a Waved Albatross, don’t go from January to April, because they won’t be there. If you want to see a specific animal, your tour company should be able to tell you when is the best time to go.
Tourism
If it’s your plan to go to the islands and either island-hop or try to find a good last-minute deal, you’ll want to do so during low tourist season. Try May-early June or late September-October. Early December is also a good time to go. If you go during high season, hotels and last-minute deals will be much harder to find.