The Church gave you the scripture. Some enemy. I may have failings, but reading "water" and seeing "flesh" is not one of them.
The RCC did not give the scriptures to anyone.
All church councils only recognized what local churches had already accepted as scripture and the local churches were not under any obligation to accept incorrect views on the scriptures.
Christians had the scriptures despite the RCC, as they do today.
'That which is born of the flesh is flesh, and that which is born of the Spirit is spirit'(Jn.3:6).
Christ explains the earlier verse in which Nicodomus asks if he must go back into his mother's womb to be 'born again'.
That is the flesh that Christ is referring to the intial birth that is connected to the water of the womb.
Just as Christ came by water and blood (1Jn.5:6), showing His two natures, human (water) and blood, God's blood (Acts.20:28)