Authorities seized eight-and-a-half tons of marijuana and 327lbs of cocaine in connection with the discovery of the tunnel.
Three men who authorities say worked as drivers were charged with possession of marijuana and cocaine with intent to distribute. US lawyer Laura Duffy said they face prison sentences between 10 years and life if convicted.
The tunnel, which zigzags the length of nearly six American football fields, links warehouses in Tijuana and San Diego's Otay Mesa industrial area. The area has many nondescript warehouses, making it easier to conceal the loading of drugs.
The tunnel was shut down before any drugs made it through. The San Diego warehouse had been under surveillance after a tip-off from an informant.
More than 75 underground passages have been found along the border since 2008.