San Diego International Airport: For Downtown, take MTS Route 992, the Flyer, from either terminal to Santa Fe Depot: about 10–15 minutes and roughly $2.50. It beats a $30-plus taxi for anyone staying downtown. For Old Town and onward Trolley connections, use the free San Diego Flyer shuttle to Old Town Transit Center; use rideshare instead if your hotel is at the beach or in La Jolla, where transit becomes slow and indirect.
Tijuana International Airport / Cross Border Xpress: If Mexico is your starting point, use the pedestrian-only CBX bridge into the U.S. side rather than crossing at San Ysidro by car. The bridge costs roughly US$20–27 each way (less as a return ticket) and avoids the notoriously variable vehicle queues; from the CBX terminal, take a rideshare into San Diego. You still need the documents required to enter both Mexico and the United States.
Santa Fe Depot: Amtrak’s Pacific Surfliner and the COASTER arrive in the useful part of town: Downtown, by the waterfront and near the Trolley. Do not take a taxi merely to reach central hotels; most are a short walk or a very short rideshare away. This is the sensible rail arrival from Los Angeles and Orange County, though delays and a roughly three-hour Los Angeles–San Diego journey make it a travel day, not a quick transfer.