Trinity Gay, 15, died after being shot in the neck amid an exchange of gunfire between two parked vehicles at a restaurant in Lexington, Kentucky.
Police do not believe Trinity was in either of the vehicles involved in the early Sunday morning shootout.
On Monday night, thousands of people held a candlelight vigil in her memory.
Chazerae Taylor, 38, and his 19-year-old son D'Markeo, face charges for wanton endangerment.
Bail was set at $5,000 (Â£4,000) for each of them.
Another man, Dvonta Middlebrooks, 21, was charged with wanton endangerment and possession of a firearm by a convicted felon.
His bail was set at $12,500.
All three men allegedly fired multiple shots during the incident.
On Monday night, Tyson Gay led thousands of mourners in a candlelight vigil for his daughter at her Kentucky high school.
Gay said he was numb from crying over Trinity's death as he stood on the track at Lexington's Lafayette High School, which he also attended as a boy.
"I want you guys to love each other, have peace and protect each other," said Gay.
"That's what Trinity would have wanted. Life is not a joke."
Trinity was following in her father's footsteps as a talented sprinter at the school.
She had placed in the top five for several events in the Kentucky state competitions.
Gay said he believed his daughter was an innocent bystander caught in the crossfire of the shootout that erupted in the early hours of Sunday between two vehicles.
Trinity was pronounced dead less than an hour later at the University of Kentucky Chandler Hospital.
"She was a beautiful person, very outgoing, athletic, always wanting to accomplish something," Debra Conley, Trinity's grandmother, told the Lexington Herald-Leader newspaper.
USA Track and Field have also tweeted their condolences.
Tyson Gay is the joint second-fastest 100m runner of all time, behind Usain Bolt.
He participated in the last three summer Olympic games and was part of the US 100m relay team at the Rio Olympics.
He won a silver for the 4x100 meter relay in London 2012, but that medal was stripped when he tested positive in 2013 for a prohibited substance and was banned from competition for a year.
Three men charged in the fatal shooting of Trinity Gay, daughter of US track athlete Tyson Gay, have pleaded not guilty in a court appearance.