Fajardo is where the east coast does its business: the ferry terminal for Vieques and Culebra, the biggest marina in the Caribbean at Puerto del Rey, and the departure point for day sails out to the cays offshore.
The reason to stay rather than pass through is Laguna Grande. It is one of three bioluminescent bays on the island, and the only one you reach by kayak through a mangrove channel — twenty minutes of paddling in the dark before the water starts to light up around the blade. The dinoflagellates that do it, Pyrodinium bahamense, need the mangroves and the narrow mouth of the lagoon to stay concentrated, which is why so few bays anywhere manage it. Go on a night near the new moon; a full moon washes the effect out entirely, and the operators will tell you so when you book.
Las Cabezas de San Juan on the headland north of town packs seven ecosystems into a small reserve — dry forest, mangrove, the lagoon, coral offshore — around an 1880s lighthouse, and is run by the island's conservation trust with visits by reservation.
The cays a short sail out — Icacos, Palomino, Palominito — are the day-trip standard: sand, clear water, snorkelling on the reef, and a great deal of rum on the way back.