Esteban Santiago, 26, is accused of opening fire at Fort Lauderdale airport, killing five people and injuring six others.
He is charged with carrying out an act of violence at an international airport resulting in death, which carries a maximum punishment of execution.
Mr Santiago also faces lesser weapons charges.
The suspect, who is in custody, told agents he had planned the attack and bought a one-way ticket to Fort Lauderdale, according to court papers.
Authorities said they did not know why he chose this target and that terrorism had not been ruled out.
"Today's charges represent the gravity of the situation and reflect the commitment of federal, state and local law enforcement personnel to continually protect the community and prosecute those who target our residents and visitors," US Attorney Wifredo Ferrer said.
Mr Santiago is said to have used a semi-automatic handgun that he apparently legally checked on a flight from Alaska.
Officials were also looking whether mental health problems played a role after it emerged that the suspect had been referred for a health assessment by the FBI.
Last November, Mr Santiago walked into an FBI office in Alaska in an agitated and incoherent state, the FBI and Anchorage police said.
He was carrying a loaded magazine but had left his handgun in his car, with his newborn child.
During the later mental health evaluation, he told the FBI he was hearing voices and believed he was being controlled by a US intelligence agency.
His gun was confiscated but the authorities found no wrongdoing, and it was returned in December. It is not clear if this is the same gun that he is accused of using in the attack at the airport baggage claim area.
An official list of the victims has not been released but families and friends have confirmed some of the identities.
Olga Woltering: A Georgia resident originally from Ipswich in eastern England.
A devout Catholic in her 80s, she was named as a victim by her Atlanta church, the Catholic Church of the Transfiguration. It described her as a "joyful, loving, caring and committed" person.
"This is a horrible tragedy for everyone here at Transfiguration, especially because Olga was so loved," it said.
Ms Woltering, from Marietta near Atlanta, was in Florida on her way to join a cruise to celebrate her husband's 90th birthday. He was unharmed in the shooting.
Terry Andres: The 63-year-old from Virginia Beach, Virginia, was a volunteer fireman. He and his wife had flown to Fort Lauderdale for a Caribbean cruise. He was named as a victim by friend Jessica Winbauer.
She told AP news agency that the death had shocked the community.
Michael Oehme: The 57-year-old Iowa man was named by his sister, Elizabeth Oehme-Miller. He was supposed to go on a cruise with his wife, she said.
Mr Oehme was a land surveyor and owned his own business. His wife was in hospital with injuries from a gunshot wound to the shoulder.
Shirley Timmons: The 70-year old from Senecaville, Ohio, was travelling with her husband, Steve, to join the rest of the family for a cruise, according to her grandson Steve Reineccius.
Wile FM reported that her husband was shot in the head and underwent emergency surgery at a hospital in Fort Lauderdale, where he was in critical condition.
Mr Santiago is a former member of the Puerto Rico and Alaska National Guard, according to the Pentagon.
He served in Iraq from April 2010 to February 2011, and ended his service in August 2016.
His aunt told a local newspaper he had "lost his mind" while serving in Iraq, and his brother said he had been receiving psychological treatment recently.
US media reported that he had received a general discharge from the Alaska National Guard for unsatisfactory performance.
Flying with firearms is legal in the US as long as the guns are kept in a locked, hard-sided container as checked baggage only, under rules of the Transport Security Administration (TSA). Ammunition is also allowed only in checked luggage.
The attack was the latest in a series of mass shootings in the US in recent years, carried out by people who had easy access to weapons under US gun laws.
Last year, in the worst shooting in recent US history, a man apparently inspired by so-called Islamic State killed 49 people at a gay nightclub in Orlando, Florida.
The man suspected of carrying out a deadly shooting at a Florida airport has been charged by prosecutors.