You should allow yourself at least 90 minutes to explore El Morro. There is about a half-mile of hiking to be done in the fort, with a couple of steep climbs if you wish to experience all five accessible levels (the sixth level is not open to the public.) You can and should carry drinking water with you, and there is a small refreshment shop inside. The museum area is quite good, although rather small; the gift shop is fair at best. Here is the link to the National Park website: http://www.nps.gov/saju/morro.html
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