Gundogan is tied to City until 2020 and shone in victory over Watford.
"I think Gundogan made an incredible game, an incredible player in all senses," Guardiola said.
"I said in the press conference we would like to but it depends on the club and him so I don't know," the City boss said of Gundogan's contractual situation. "Hopefully he can stay.
"I would prefer him to stay but at the same time I want to feel he wants to stay too.
"If he doesn't want to stay he has to leave. But we would like to continue. Next season he has a contract and a longer time together.
"I said before if he wants to stay, we will talk to him and we can sign the contract.
"We signed the contract with Kevin [De Bruyne] in a few days, with other players, with Gabriel [Jesus]. But he doesn't want right now so we will wait.
"When he wants it, we will be here."