In John chapter 6, John isn't talking about regeneration by water baptism; he's talking about the Eucharist.
And, since he isn't saying anything about regeneration by water baptism in that passage, you can not say that it proves anything about water.
So, of course nothing in John 6:36 doesn't say that water ever made anyone holy or regenerated. Why would it? That's a totally different topic from what John was speaking of there.
Jesus specifically DID SAY that you have to be born again (regenerated) in water AND in spirit at John 3:3-5.
Jesus answered and said to him, “Most assuredly, I say to you, unless one is born again, he cannot see the kingdom of God.”
Nicodemus said to Him, “How can a man be born when he is old? Can he enter a second time into his mother’s womb and be born?”
Jesus answered, “Most assuredly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God.
In THAT passage, Jesus IS talking about being born again (regenerated) in water AND in the Spirit.
You cannot refute a passage that does talk about regeneration in water and Spirit by quoting another passage that does not say anything whatsoever about regeneration.
You have taken one verse out of its context and tried to force it to say something it was never meant to say.