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You can join a horse (or mule) tour in the nature park. Most of the agencies in town should offer these tours when asked.
Poor Man's Galapagos
Several tour agents organise trips (1½-hour boat ride, lunch included). On the island you will be able to see plenty of blue and red footed boobies, frigate birds, colorful fishes, sea turtles, and if you're lucky, sea lions. The tour is combined with snorkeling and whale watching trips, if it's the right season. The humpback whale season is from June to September. Diving is also possible. You'll pay $1 extra for the use of the pier. The trips to the island are heavily regulated by the local authorities so it does not seem to be possible to hire a local fisherman to take you to the island.
The national park has several entrances and "themes". One of them is the Frailes which is free, there is a nice path that goes through miradors and beaches and end in the Frailes beach where you can swim and snorkel. Another is the Agua Blanca ($5pp) where you'll have a guided visit of the (small) archeological museum, a visit of the lands and finally a bath in sulfur water. You can go to either by taking any bus going north for 50¢.