Getting permission to bring your own yacht into Galápagos waters is genuinely one of sailing's great bureaucratic endurance sports. Ecuador requires a zarpe from a mainland port — usually Salinas or La Libertad — advance authorisation from the Galápagos National Park, and an ingala permit that limits your stay and restricts where you can anchor. Even then, an official park naturalist guide must accompany you at every landing site.
None of this should put you off, but go in clear-eyed: paperwork done months ahead, not weeks.
The passages themselves are substantial. From Salinas to San Cristóbal runs roughly 900 nautical miles, typically southwest, and you'll be working through a confused stretch where the cold Humboldt Current meets the warmer Panama Flow.
Winds are frustratingly light and variable for much of the crossing — June through November gives you more reliable southeast trades, while the wetter season from January to May brings calmer, glassier conditions that some sailors prefer for the wildlife diving. Expect motoring. Carry ample fuel.
Once inside the archipelago, day sailing between islands is the real reward. The inter-island channels run with strong currents, often two to three knots, which you need to read carefully for timing your approaches. Puerto Ayora on Santa Cruz is the logistical heart — provisioning is possible but expensive and often limited, so arrive with full stores from the mainland. Anchoring is tightly regulated; you'll be directed to designated spots.
The upside is that those anchorages put you metres from sea lions on the dock, blue-footed boobies overhead, and marine iguanas completely indifferent to your presence.
Most sailors choose a fully crewed liveaboard charter rather than a bareboat — unless you have thorough passage-making experience and extraordinary patience for officialdom.