Francisco Jose Garzón Amo was driving the high-speed train that went off the rails and ploughed into a siding near the northwestern city of Santiago de Compostela on July 24th 2013.
Investigators found that Garzón was talking on the phone shortly before the Alvia-type train crashed as it hurtled round a sharp bend at 179 kilometres per hour (110 mph) - more than twice the speed limit for that stretch of track.
The crash raised questions about the railway's safety systems. Judges interrogated various officials from the state railway company Adif, but dropped charges against all of them.
Garzón faces 80 counts of reckless homicide and 144 counts of injury and is the "only person charged", the Galicia regional high court said in a ruling on Wednesday, updating an earlier death toll of 79.
Victims' families say the driver was not the only one responsible and have demanded a parliamentary commission to investigate the causes of the crash.
The court said experts had agreed that excessive speed was "the sole cause of the accident".
It said there was no criminal liability for the fact that the track lacked the latest speed control systems.
"The direct and immediate cause, which decidedly set in motion the unfortunate accident... was excessive speed," the court said.
But it acknowledged that "safety on the line could have been better".
Wednesday's ruling can be appealed and the judge will later rule on whether to put Garzón on trial.
Garzón last year wrote a letter begging the forgiveness from the victims, saying he was "destroyed" by the tragedy.