Most people get around the islands by organized boat tours, but it’s entirely possible to visit some of the islands independently. Santa Cruz, San Cristóbal, Santa María (Floreana) and Isabela all have accommodations and are reachable by interisland boat rides or flights (which are pricey). Keep in mind however that you’ll only scratch the surface of the archipelago’s natural wonders traveling independently.
Ingala (Puerto Ayora 05-252 6151), a government-run company, operates passenger ferry services aboard the Ingala II. It goes from Santa Cruz to San Cristóbal Monday, Wednesday and Friday and from Santa Cruz to Isabela about twice monthly (usually on a Friday) and once a month from Isabela to Floreana. The office in Puerto Ayora can give you up-to-date details, as can the Camará de Turismo (tourist information office) in Puerto Ayora. The departure times change periodically.
Fares are $50 for foreigners (sometimes cheaper in low season) on any passage and are purchased either on the day before or the day of departure. Ask around in Puerto Ayora and Puerto Baquerizo Moreno for private companies that ply the same routes daily or weekly; these are cheaper and faster but also tend to be smaller and more sensitive to rough seas.
The small airline, EMETEBE(Puerto Ayora 05-252 6177, San Cristóbal 05-252 0036, Puerto Villamil 05-252 9155, Guayaquil 04-229 2492), flies a five-passenger aircraft between the islands. It offers two to three flights a week between Baltra and Puerto Villamil (Isla Isabela), between Baltra and San Cristóbal, and between San Cristóbal and Puerto Villamil. Fares are about $120 one way, and there is a 13kg baggage limit per person (although this is flexible if the plane isn’t full).