Officials said Walkes was found unconscious and transported to shore by Miami Fire Rescue where he received CPR. Walkes died Thursday morning, officials said.
Walkes, an Englishman who first joined United at 19 years old from Tottenham Hotspur's youth ranks, played last season with Charlotte FC.
He was just a few weeks shy of his 26th birthday on Feb. 8.
"We are deeply saddened to share that Anton Walkes has tragically passed away this morning. May he rest in peace," Charlotte FC wrote on Twitter.
Atlanta United, in a statement, said: "We are heartbroken to learn of the tragic passing of Anton Walkes. An inaugural member of Atlanta United, Anton was the epitome of a great teammate with a personality that lit up every room he entered. He will be deeply missed by all of those who knew him. On behalf of everyone at Atlanta United, we send our deepest condolences to Anton's family, friends and Charlotte FC."
The Atlanta United account replied with two heart emojis.
A Charlotte club statement remembered him as a "truly incredible father, loving person and outstanding human being."
Walkes played 20 games with United in their inaugural season in 2017 before returning to England, where he played three seasons with Portsmouth.
He returned to the U.S. and MLS in 2020, becoming a fixture for United across that season and the next in 2021.
He went to Charlotte last year and was a regular for that club in their inaugural MLS season.
The MLS league account wrote on Twitter: "There are no words to describe the sorrow of everyone in Major League Soccer today after learning of the tragic passing of Anton Walkes of Charlotte FC. Anton was a talented and dedicated player who was loved by his teammates and fans."
The club he spent several seasons with in England, Portsmouth, wrote: "Everyone at Portsmouth Football Club is extremely saddened to learn of the passing of Anton Walkes. Our thoughts are with his friends and family at this difficult time."