Puerto Rico is small enough to drive across in three hours and big enough to hold a whole different trip outside San Juan. These are the family stops I would build a second week around, or trade a resort day for.
Vieques and the bio bay
Mosquito Bay on Vieques is the brightest bioluminescent bay in the world. You kayak out after dark on a moonless night, dip a paddle, and the water lights up blue. Kids need to be able to sit in a tandem kayak for an hour, so around six and up. Tours use clear bottomed kayaks and electric boats for younger kids. Get there by a short flight from San Juan or the ferry from Ceiba. Vieques also has wild horses on the roads and empty beaches inside the old navy land.
Culebra
Flamenco Beach is regularly named among the best beaches anywhere and it earns it. A long curve of white sand, calm turquoise water, and a couple of rusting tanks at one end that kids find fascinating. There are kiosks for lunch and a campground. Day trip by ferry or plane from the main island, or stay a night in one of the small guesthouses. Snorkeling at Tamarindo beach usually turns up turtles.
The west coast
Rincon is the surf town, laid back with a lighthouse park where whales pass in winter. Nearby Crash Boat beach in Aguadilla has a pier to jump from and calm water for smaller kids. It is a two and a half hour drive from San Juan and it is worth two or three nights.
Camuy caves
In the northwest, a huge cave system with a trolley ride down into a sinkhole and a walk through a cathedral sized chamber with a river below. Tours reopened after years of repairs. It is cool underground and suits every age.
Ponce and the south
The Ponce Art Museum, a colorful old fire station on the plaza and, up the road, the Toro Verde zipline park with one of the longest ziplines in the world for teens.
Practical
Rent a car, avoid driving at night on mountain roads, and book the bio bay tours and island ferries well ahead in school holidays. The ferry to Vieques and Culebra sells out and the plane is often worth the extra.
Planning Puerto Rico with kids? Start with the full Puerto Rico family travel guide, or send me the ages and the dates and I will come back with what is really available.
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