Setting aside the idea about natural birth (which does not appear credible to this student based on the following information: 1) Jesus nowhere describes physical birth in this way, nor do other NT writers; 2) Jesus and other writers do describe physical birth in a different way, consistently; 3) the person Jesus is speaking about has already been born, Jesus is saying he must be born again; 4) The Gk. word is, as noted above, water in a stream, river, fountain) I would tentatively rule out that option, and look for other options. It would be necessary to go outside the passage IMO to find the answer.
Jesus spoke of water in a symbolic sense in a couple other places in John, identified in ch. 7 or so as the Holy Spirit. However, in ch. 3 He also mentions the Spirit, so in that case water would appear to be something different. Paul the apostle describes the washing of regeneration through the Word, although NOT identifying the Word symbolically as water. BUT Jesus does not so describe the Word. In John's gospel, Jesus describes the Word as the Word, ho logos. Never does He characterize the Word as water. I therefore tentatively rule out both the Spirit and the Word, for those reasons.
Next thing I would look into is any other place in John's gospel where water and the Spirit are specifically mentioned in connection. I find one such place in ch. 1, where Jesus was baptized by water and the Holy Spirit descended upon Him. I do not recall any other places in John. I would then inquire if baptism by water pertains to being regenerated. I do not find a discourse on that subject presented by Jesus, only the charge to His disciples to go into all the world, baptizing in the name of the Father, Son and Holy Spirit. I therefore must go outside John's gospel to find such a discourse. I do find one on it by Paul, in Romans 6. Paul says:
I see here described, dying to the old life and starting a new life, that is, a regeneration. And I see this regeneration, this beginning a new life, connected by Paul with baptism. Without a doubt, then, baptism is connected Scripturally with a regeneration, ending or dying to the old life, and beginning a new life, with Christ living in us and through us. Is this the same regeneration that Jesus spoke of? Is there more than one regeneration? This might be a question to look at.
To summarize, then:
1) Jesus spoke of regeneration by water and the Spirit, Jn. 3:5.
2) Water baptism is connected with regeneration, Rom. 6:1 - 7, and with the outpouring of the Spirit, , Jn. 1--thus water and the Spirit.
Are these one and the same events, or is there more than one regeneration? I see the following match-up:
Regeneration ====== Regeneration
Water =========== Water
Spirit ============ Spirit
Seems so far like one and the same event.
Dave