Because of all the restrictions, some guide books suggest to skip the islands all together. Skipping the islands would save you about $200, as harbor and immigration fees are quite high.
We would recommend not to miss out on these islands as they are a convenient stop over and even a short stop, particularly in Wreck Bay, San Christobal, is always worth while, if only for the nice sea-lions that will visit your boat.
The ports that can be approached from outside the islands are: Puerto Ayora, also called Academy Bay, on the island of Santa Cruz, and Puerto Baquerizo Moreno, also called Wreck Bay, on the island of San Christobal.
Standard supplies are all available in both places and repair facilities for engines as well as spares seem even better than in Panama, as the many tour boats need to be kept going. Diesel is significantly cheaper than in Panama. At the gas station a U.S. Gallon of diesel costs $1.05, brought to the boat we paid $1.30 in Christobal and $1.80 in Puerto Ayora, where all prices seem a little bit higher.
Short trips into the island as well as boat excursions or dive trips are available in both Puerto Ayora or Christobal, with a bigger choice in Puerto Ayora.
Fees are as follows:
International arrival $0.014 per ton or a minimum of $10
Zarpe $0.014 per ton or a minimum of $10
Frequency use $15
Channel Access $0,41 per ton
Anchorage $2.21 per ton
Contamination fee $15
International arrival Navy $3 per ton
Immigration $15 per boat for entry and again for exit
(for our 18t boat we paid roughly $150 when clearing into Christobal) I think even for a short stay you would pay those fees.
You can easily at no extra cost get a permit to stay up to 20 days, which is usually more than you need. Just ask the harbor master, and immigration usually gives you a full month anyway. Like with a short stay you can go onto tour boats and explore the island.
One day tours are typically around $70 per person and include breakfast and lunch on board. As said before, more choices, especially for day trips are available in Puerto Ayora (Academy Bay). Trips of several days, with accommodation on the tour boat seem to cost around $120 to $400 depending on the vessel.
The safer place to leave your boat alone at anchor would definitely be Wreck Bay, San Christobal, with excellent holding and lots of space. In Puerto Ayora there is always a swell running so that all boats lay to bow and stern anchors. Especially towards shore, where you would usually drop your stern anchor the bottom is sharp lava rock with a few patches of mud, so use chain as many ropes have been cut by those rocks. Normally you have to stay at the place you chose for clearing in until you leave.
Once you clear out you can usually get permission to stop for a few days in a secondary port, typically Vilamil on Isablella island, which is on the way towards the Marquesas. The only other port that could be visited with such an arrangement would be Puerto Velasco Ibarra on the island of Floreana. But there is nothing in the village and the anchorage is exposed and rolly.
Only if you can get both harbor masters agree, you may get special permission to go from Christobal to Puerto Ayora or vice versa. An agent may be able to arrange that for you.
With a cruising permit you can move freely between the four ports, so that you have more flexibility with you itinerary. To get a cruising permit you have to apply for it before you arrive in the islands. From what we understand there is no limitation on those, you just need to get the process going no later than two weeks prior to your arrival. This is best done by getting an agent and faxing him, copies of ships papers and passports.
The price for a cruising permit is again dependant on tonnage and the agent will add some percentage on top of it. We paid the agent $150 for the permit for our 18t boat. A 55 ton boat was charged $300.
We also found out that every time you move from one port to another, you need to clear in and out and that all costs you every time, between $20 in the small ports and around $50 in the main ports.
Once you have a cruising permit, you can apply for a permit to visit the national park areas with your own boat. You will need to hire a licensed guide and take him with you, and you will also file a detailed itinerary beforehand. Other than that and the high price, there is really no other limitation.
Again it is best to let your agent do the arrangements as it involves some paper pushing and you need to write a letter to the chief of the park essentially saying that you are a nice guy and that you will certainly respect all park rules.
The fee for the park is very high: $200 per person per day. To this you need to add the fee for hiring your guide which would be between $150 and $200 per day. We hired our guy through our agent and were very pleased.
While this sounds very expensive, it seems within reason when compared to the cost of going on a tour boat for several days. Only with your own boat or by going for a few days onto a tour boat, will you be able to reach some of the nicest, but more remote places. And then you have your guide exclusively for yourself and you can do your visits to the best places when it is not crowded. And finally you don't have to worry all the time whether your boat is still safe.