You can visit the Galapagos any time of the year as there is always something wonderful happening in the Islands, especially with wildlife’s behavior and natural events.
From mid-June to early-December you have a mixture of warm and rain (afternoon showers), and Ocean waters are warmer and calmer due to the “El Niño” current. From mid-December to early-June is the cool/dry season on land and Ocean, especially because of the passing of the “Humboldt” current through the Archipelago.
It depends especially on the level of comfort and facilities on board you are looking for:
First, you must get to Ecuador Mainland. Make sure you arrive to Quito or Guayaquil at least one day before your departure to the Galapagos; there are no direct connections with international flights and flights to Galapagos Islands depart from mainland Ecuador early in the morning from Quito and/or Guayaquil.
Visitors arrive by plane from Mainland (flight takes about 2 ½ hours) with three main Airlines: AVIANCA, LAN and TAME and arrive to Galapagos to one of its two Airports: One in Baltra Island and one in San Cristobal.