The Galápagos has two airports: Seymour Airport on Baltra Island (serving Puerto Ayora on Santa Cruz) and San Cristóbal Airport on the eastern edge of Puerto Baquerizo Moreno. Both receive daily flights from Quito (around 3 hours) and Guayaquil (around 2 hours) on LATAM and Avianca. Fares vary significantly by season and how far in advance you book; booking early is advisable during high season (June-August and December-January).
All passengers entering the Galápagos must pay a conservation fee at the mainland airport before departure — at time of writing, USD 100 for most foreign visitors (USD 50 for residents of Ecuador and citizens of certain Andean nations). There is also a transit card fee of around USD 20 payable on arrival. These fees fund the National Park and the Galápagos biosecurity system; inspectors check luggage for prohibited foods and plants before you board.
Inter-island boats (lanchas) run between Puerto Baquerizo Moreno and Puerto Ayora on Santa Cruz roughly twice daily. The crossing takes about 2.5 hours and costs around USD 30 each way. Seas can be rough, particularly in the dry season. There is no inter-island air service between the two main towns, though some cruise itineraries use chartered flights.