Water taxis from Belize City are the main connection for budget travellers. San Pedro Express and Ocean Ferry both operate from the Marine Terminal in Belize City, with departures throughout the day from roughly 8am to 5pm. The crossing takes about 1.5 hours and costs around BZ$30–35 each way. Caye Caulker is a stop along the way and takes about 45 minutes from San Pedro.
Flying is dramatically faster. Tropic Air and Maya Island Air have multiple daily 15-minute flights between San Pedro and both Belize City International (for connections onward) and the smaller Philip Goldson Municipal Airport. Fares are around US$50–80 each way. If you are arriving from overseas with a connecting flight the same day, flying is the only sensible option. The airstrip in San Pedro is right at the edge of town — you walk from the plane.