The three indicted were Sgt. Shawn Gibson, Capt. Philip Wolford and Lt. Col. Philip de Camp, all from the U.S. 3rd Infantry, which is based in Fort Stewart, Georgia.
Spanish Judge Santiago Pedraz asked American authorities to notify them of the indictment.
In the five-page indictment, Pedraz charged the three men with homicide and "a crime against the international community." This is defined under Spanish law as an indiscriminate or excessive attack against civilians during war time.
The journalist, Jose Couso, who worked as a cameraman for the Spanish television network Telecinco, died on April 8, 2003, after a U.S. army tank crew fired a shell at a Baghdad hotel where journalists were staying. Taras Portsyuk, a Ukrainian cameraman for Reuters, was also killed.
Following the incident, then-U.S. Secretary of State Colin Powell said American troops opened fire after drawing hostile fire from the hotel. He said a U.S. review of the incident found the use of force was justified.
Pedraz has issued several arrests warrants against the three soldiers, but the United States has made clear it will not hand them over.
The soldiers still run the risk of arrest under a Spanish-issued international warrant should they travel to any country that has an extradition accord with Spain.
Under Spanish law, a crime committed against a Spaniard abroad can be prosecuted here if it is not investigated in the country where it was allegedly committed.