Some say that water here means baptism. But that is unlikely since Christian baptism hadn't yet been instituted.
In fact, Christian baptism is being instituted in this very verse. This is what institutes Christian baptism, straight out of the mouth of the Savior.
If this verse did mean baptism, then the only kind that it could have been at that point was the baptism of repentance administered by John the Baptist
This is false. John 3:22ff makes it clear that Jesus' disciples were baptizing under his supervision (it is ambiguous on whether Jesus himself baptized; 3:22 says he did, 4:2 says he didn't, but they may not have been talking about exactly the same time period), and they were not administering the baptism of John the Baptist, because John says clearly in Jn 3:27-30 that Jesus' ministry is superior to his own.
It is my opinion that the water spoken of here means the water of the womb referring to the natural birth process.
Jesus is not really in the business of teaching obstetrics. But look at this sentence carefully. See the highlighted words?
In an earlier post, you wrote:
When your beliefs or doctrines are supported more by 'writtings of early Church fathers' then the Scriptures, you are at least making them equal to Scripture, if not elevating them to be more important then Scripture.
What about when your beliefs are supported mostly by the opinions of a website like CARM?
Aren't you doing precisely what you reject us for doing?
Concretely, consider this contrasting opinion about John 3:5:
"And He says, 'Unless a man be born again' -- and He adds the words 'of water and the Spirit, -- he cannot enter into the kingdom of God'. He that is baptized with water, but is not found worthy of the Spirit, does not receive the grace in perfection. Nor, if a man be virtuous in his deeds, but does not receive the seal by means of the water, shall he enter into the kingdom of heaven. A bold saying, but not mine, for it is Jesus who has declared it."
That's St. Cyril of Jerusalem, writing around AD 350 (Catechetical Lectures, No. 3, paragraph 4).
What makes your opinion, or CARM's, superior to, or more trustworthy than St. Cyril's? Why should I believe them, and reject him? How is CARM's opinion about Scripture any less a "tradition of men" than St. Cyril's? How is what you are doing any more "scriptural" than what we do?
Don't think that I'm picking on you in particular, BTW. This conundrum is present throughout Protestantism. For example, in the 1662 edition of the Anglican 39 Articles, we read:
"General Councils may not be gathered together without the commandment and will of Princes. And when they be gathered together, (forasmuch as they be an assembly of men, whereof all be not governed with the Spirit and Word of God,) they may err, and sometimes have erred, even in things pertaining unto God. Wherefore things ordained by them as necessary to salvation have neither strength nor authority, unless it may be declared that they be taken out of holy Scripture."
Being as I don't have to worry about the King's good men battering down my door on account of my Romish sympathies ;-), I will ask the obvious naughty question:
If councils "do err," and "have erred," where's the guarantee that the 39 Articles don't err? What's to guarantee that they don't err precisely in saying that councils err, for that matter?
As for their appeal to Scripture, that simply begs the question: who gets to decide, authoritatively, what Scripture means? "Unless it may be declared that they be taken out of holy Scripture" ... declared by whom? With what authority? And what if I disagree with his declaration?
The whole claim is simply a recipe for anarchy, which inevitably circles back on itself and does the same thing it accuses Catholics of doing: it goes to fallible men to decide what infallible Scripture is really telling the Church. The only real difference is that you choose your own "Pope", and mine is chosen for me.