If you are going to Las Grietas or one of the hotels on the south side of the harbour you should take a water taxi across the harbour. The taxi boats leave from the new pier and if there isn’t one there when you arrive, one will soon come. As soon as there is one passenger they leave, so you don’t have to wait for other people to fill up the boat. The fare across the harbour is $0.60 (July 2011).
Update June 2013: The fare across the harbour is still $0.60. After 7pm it cost $1.
The first time I arrived to Baltra was with plane and I was going on a cruise. We (the people going on the cruise) were met at the airport by our guide and, as we were visiting the highlands on Santa Cruz and Charles Darwin Research Station before boarding the boat, we took a bus from the airport to Canal de Itabaca. Frequent ferries are crossing the canal, and on the other side our bus was waiting. The second time I arrived to Baltra was in the end of the cruise when we were all taken to the airport. I was not flying back to the mainland, but was going to Isla Isabela.
From Baltra Airport I took one of the free buses going to the canal. It is a short bus ride, maybe 10-15 minutes. Canal de Itabaca is the narrow canal between Isla Baltra and Isla Santa Cruz. Here you put your bags on the flat roof of the ferry, before boarding it. Tickets for the ferry is sold onboard and I paid $ 0.80 going to Santa Cruz, but only $ 0.50 going the opposite way almost a week later. At the dock on the Santa Cruz side of the canal I immediately found a bus to Puerto Ayora. My big backpack was put on the roof and I went inside to take a seat. Tickets were sold on the bus and it was $ 1.80 (July 2011). To Puerto Ayora it took less than an hour and in Puerto Ayora the bus stopped on Av Charles Darwin, just opposite the harbour. You can also take a taxi from Canal de Itabaca to Puerto Ayora and it is $15 (July 2011).
When it was time to go back to the airport I took a taxi from my hotel in Puerto Ayora to Terminal Terrestre, from where the buses leave. The taxi was $ 1.00. I arrived to the bus terminal at 8am and the next bus to Canal de Itabaca was leaving at 8.40, so they are not very frequent.
Before coming to Galapagos I had read that it is good to buy the ticket for the speedboat a day in advance during high season. As I visited in July and was going to be aboard a boat the day before my departure I was a bit worried not to get a ticket, but the travel agent I had booked the cruise with luckily made a reservation for me.
The office of Cabomar, where I was going to get the ticket, was just one minute away from where I arrived to Puerto Ayora with bus, by the harbour. I paid for the ticket, which was $25 one way (July 2011). The speedboat for Villamil leaves Puerto Ayora at 14.00 every day and I still had some time, so I left the backpacks at the office and went to withdraw money from an ATM and to have lunch.
I went to the harbour half an hour before the boat was going to leave and people were already standing in a queue to have their bags checked.. You are not allowed to bring seeds and fruits between the islands. So there is a control before you travel.
On board we were told to put on our life jackets and we all got a bottle of water and some caramels. I think this was because it was a bit bumpy and at least two people threw up during the journey.
After two hours we arrived to Puerto Villamil. While I was standing on the bridge waiting for my luggage I was very surprised to hear my name called out. It was a taxi driver who were going to take me to Hostal La Jungla where I had made a reservation. I didn’t pay for the taxi ride, but the driver had a few other paying customers going to other hotels.
The boat back to Puerto Ayora leaves already at 6am and as you have to be at the harbour in time, to once again have your bags controlled and to pay the tourist tax ($5) it will be a very early morning. Crossing over to Puerto Ayora the sea was calm and we didn’t have to put on the life jackets. And we didn’t get water or caramels this time. We arrived to Puerto Ayora around 8.30.
In Puerto Ayora I talked with some people who had taken an afternoon boat from Puerto Villamil to Puerto Ayora. It had been one of the daytrip boats going back to Puerto Ayora and the life jackets on board that boat had been very poor and the engine broke down just before they arrived to Puerto Ayora. So it might be better to take the regular speedboat.
Update June 2013: Besides the boat leaving Puerto Ayora at 14.00 there is now also a boat leaving at 7.00 in the morning. The price is $30. The boats are now leaving from the new pier.
Transport options to Puerto Ayora are straight forward. All flights come from Quito via Guayaquil and land at a strip on the island of Baltra which happens to be as close to the island of Santa Cruz as to let you believe that the body of water separating them might be a canal, not a channel. Whatever its nature, one has to navigate it on board of a ferry which takes about five minutes and then proceed to the cowboy embrace of the local taxi yahoos for 15USD or just keep his cool and join the other easy-going passengers in a well-kept bus for 3USD. The distance to Puerto Ayora is 42km and it takes a while but the landscape is so intriguing and ever-changing that one hardly notices how the time flies. As all the other islands, this one is no exception in the way the winds and the moisture carried by them sculpt the flora on its slopes. The northern sections are arid and almost desolate, while the peaks are immersed in mist and luscious, but the southern shores are green and fertile.
There are four airlines serving this route; LAN, TAME, ICARO and AEROGAL. Icaro is the newest edition and the cheapest option. It uses the planes of LAN in a code share scheme and provides you with half price for the same flight in the process. Highly recommended!