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The most famous attraction here is definitely the Bioluminescent Bay, where tiny, single-celled dinoflagellates set the waters aglow. Also referred to as the Bio-Bay, go on a moonless night to guarantee a spectacular sight. Boat and kayak tours are available, which typically last about two hours and cost between $25 and $30. In the day time, a tour of the mangroves around the bay gives a more complete understanding of how the bay remains healthy and the nature of the ecosystem that sustains it. Look for herons and flycatchers among the mangroves.
Back on land, stop by the Museo El Fort in Conde de Mirasol, a defensive fortress built in the 1800s. Today, the museum has changing exhibits portraying the art and history of Vieques, including the Spanish conquest, Taino Indian relics, early maps, and a bust of Simon Bolivar. The museum also has a small gift shop and a wonderful view of the sea and Isabel Segunda.
Another sight worth seeing is the National Wildlife Refuge, the largest Caribbean landmass of its kind. The 18,000-acre Refuge features the island’s best beaches, forests, and mangrove wetlands, and is home to several endangered species, including brown pelicans, manatees, and sea turtles.
Check out the Faro Punta Mula, a Spanish-built lighthouse from the late 1800s. Modern-day renovations have added a maritime museum that depicts the area’s history.
The Vieques conservation trust on the Malecon in Esperanza has some useful displays of artifacts and sealife native to the area. There are also aquariums in the back courtyard with 'visiting' sealife for view. You might see more there than in some snorkeling tours.
By taxi or by car you can visit the 300 year old Cieba tree near the old navy base entrance, as well as the long pier, which was originally to be built all the way to Puerto Rico main island. And throughout the western end are old bunkers that were used for weapons storage during the navy occupancy, now overgrown a bit. You can also visit the site of the 4000 year old skeleton excavated among large boulders, not far from Esperanza. There is no indication of the excavation itself now, but the boulders are unusual and impressive and native mahogany trees have been replanted around them.