After you de-plane in Baltra, you will either meet the naturalist guide leading your pre-arranged tour or you will head off individually to Puerto Ayora. If you have an organized cruise tour, you will go with your guide and boat-mates on a five-minute TAME or Aerogal bus-ride to the “muelle,” or dock, where your boat is anchored. If you have arranged a day-tour from Puerto Ayora, you will take a similar bus-ride to the “canal,” or channel, where you will meet a ferry, take a five-minute trip to Santa Cruz, and board an already-waiting tour bus.
If you are on your own and heading to Puerto Ayora, follow the day-tour groups: you can ride the same TAME or Aerogal bus to the canal (for free) and take the same ferry to Santa Cruz (80-cents one-way). Once you get across the channel to Santa Cruz, you can either catch a taxi (about $15 per truck, so try to share) or public bus ($3) to take you the final leg to Puerto Ayora. Ideally, the ferries and buses are scheduled to coincide with flights landing and taking off, so you should not have to wait long. The taxi or bus will drop you off in any of the most frequented central spots—like the main pier or boardwalk—or the hotel you specify to the driver.