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I stayed at the Fajardo Inn in March 2006 with my 13 year old son. The rooms are simple and clean at a an affordable price. The staff were very friendly and bent over backwards to make your enjoyable. They are in the process of expanding the hotel and remodeling the rooms and the pools are just glorious. The attention you receive is as if you are at a bed and breakfast but the accomadations are of a resort.
It is a must to visit the famous Flamenco Beach in Culebra Island. You do not doubt why the beach was named the 2nd most beautiful beach in the world. The town and beach are uncommercialized so don't expect a resort town. I took the 3 hour ferry ride (which cost $2) to and from the island. I would suggest to take the ($20+ airplane ride instead). So much time is wasted in traveling when you can be laying out on the beach. The ferry schedule is unpredictable and the transportation to the beach from the pier is disorganized.
The bioluminscent tour shouldn't be missed. Though it can be quite strenuous for the unathletic, it was a great experience. I suggest that you rent a car since transportation might be a bit dodgey. The water is warm and if you go on a moonless night the water will sparkle.