Stones has struggled with injuries this season and has not started a Premier League game since January.
He is set to start against Newcastle on Wednesday but Guardiola said a decision on his long-term future will be made at the end of the campaign.
"On the transfer market we speak at the end of the season," Guardiola told a news conference on Tuesday.
"I've said many times, I'm more than delighted with John as a person, as a professional, everything. What I want is the best for him. We'll speak at the end of the season about what is going to happen."
Stones, who arrived in a £47.5 million deal from Everton in 2016, has been linked with a return to Goodison Park.
The 26-year-old has managed just 20 appearances this season and Guardiola has admitted his injury problems are a concern.
"Sometimes my wish is not the wish of the players, or the wish of the situation for the club," Guardiola said.
"At the moment I will feel it, if we have to change, we'll talk to them. He's a young player and we want him to be consistent, to train and recover.
"There are players who can play every three days for 11 months. Others struggle more to be fit and we try to find the key to playing every three days. This is what we want."