San Diego International Airport: Skip a shuttle or rental car if you are staying downtown: MTS Route 992 “The Flyer” runs from both terminals to Santa Fe Depot in about 10 minutes. Budget about $2.25 per boarding, or use a day ticket if you will transfer onward. From Santa Fe Depot, downtown is walkable and the Trolley, Coaster and Amtrak connect. The free airport shuttle to Old Town Transit Center is better for Old Town, Mission Valley or Trolley connections.
Tijuana International Airport / Cross Border Xpress: A strong option for Mexico flights: use the CBX pedestrian bridge from its U.S.-side terminal into TIJ, rather than crossing at San Ysidro. The bridge itself takes minutes and avoids the often hours-long vehicle-border queues; CBX charges roughly US$20–27 one way or US$38–50 return, depending on season. You still need the correct passport/entry documents for Mexico and the U.S.
Santa Fe Depot: This is the useful rail arrival point: Amtrak and Coaster services put you at the west edge of downtown, with the Trolley and airport Route 992 outside. It is the right station for the Embarcadero, Little Italy, Gaslamp and a car-free downtown stay—not for beach communities or La Jolla without an additional bus/rideshare.