The agents said they became suspicious after the driver of the car, which was stopped at a checkpoint on Interstate 5 at 1 a.m. Friday, allegedly told them he was a U.S. citizen, according to a U.S. Border Patrol news release.
A records search revealed that he was a Mexican national, and agents arrested him for falsely claiming U.S. citizenship.
After the arrest, agents searched the man's 2011 Hyundai Elantra and found several large cardboard boxes inside the trunk and in the backseat. Each box held several wrapped packages of cocaine.
The cocaine has an estimated street value of $6.7 million, said Mary Beth Caston, a U.S Border Patrol spokeswoman.
In the 2013 fiscal year, the San Diego Sector Border Patrol seized 828 pounds of cocaine, Caston said. Friday's seizure represents more than 80% of that year's total.
The driver was turned over to the Drug Enforcement Agency for prosecution, Caston said.