Agua Expreso (787/729-8714) provides ferry service from Pier 2 in Old San Juan  to Cataño across the San Juan Bay 6 a.m.–10 p.m. The 10-minute ride costs $0.50 one way. You can also take a commuter car ferry down the Marin Pena Channel south of Santurce, which connects with the Nuevo Centro station of the Tren Urbano.
The Puerto Rico Port Authority (in Vieques 787/741-4761, 787/863-0705, or 800/981-2005; in Culebra 787/742-3161, 787/741-4761, 787/863-0705, or 800/981-2005; in Fajardo 787/863-0705 or 787/863-4560) operates daily passenger ferry service and weekday cargo and car ferry service between Fajardo  on the east coast to the islands of Vieques  and Culebra . Reservations are not accepted, but you can buy tickets in advance. Arrive no later than one hour before departure. Sometimes the ferry cannot accommodate everyone who wants to ride. The passenger ferry takes about one hour to get from Fajardo to Vieques and 1.5 hours from Fajardo to Culebra. The fare is $4.50 round-trip per person. The cargo/car ferry trip takes about two hours to get from Fajardo to Vieques and about 2.5 hours from Fajardo to Culebra. The cost is $15 for small vehicles and $19 for large vehicles.
Note that car-rental agencies in Puerto Rico prohibit taking rental cars off the main island.