“Jesus answered, Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God.”
The fundamental flaw in their argument is the unproven assumption that “born of water” means baptism. I don’t believe it does.
In all of Scripture, the term “born of water” occurs exactly once. Besides this verse, there is no other passage we can examine that might shed more light on the meaning of this term. Consequently, we only have the context of this verse to help us understand what Jesus meant by His statement to Nicodemus.
There are at least 4 possible meanings to the term, “born of water.”
First, is the possibility that it does mean water baptism. There are a few problems with this view. First, the words “baptize” or “baptism” occur approximately 85 times in Scripture. And even though this ritual is frequently mentioned, nowhere is it called, being “born of water.” If someone wants to associate this term with baptism, the burden should be upon them to do so because Scripture doesn’t make the connection.
Furthermore, to say, “one must be baptized and born of the Spirit” is antithetical to the rest of Scripture which says we are saved by grace through faith and not by any outward acts such as good deeds or circumcision (Ephesians 2:8, Romans 4:9-12)
Another possibility is that being “born of water” means being cleansed by the washing of the Word. There are a few passages that could support this idea such as Ephesians 5:26. Consider especially John 15:3 where Jesus said, “Now ye are clean through the word which I have spoken unto you.” This is reinforced in the scene where Jesus washes the feet of the disciples (John 13:9-10):
"Simon Peter saith unto him, Lord, not my feet only, but also my hands and my head. Jesus saith to him, He that is washed needeth not save to wash his feet, but is clean every whit: and ye are clean, but not all."
If a saved person is considered “washed”, “cleansed”, or “bathed” (or maybe “born of water”), then Jesus’ words to Peter are clear: we never have to be “bathed” again. If we sin – that is, “get our feet dirty” – we only need to be restored by the washing of our feet. We do no need to become saved again.
I think “born of water” fits quite nicely with the idea of being washed in the Word. But we cannot dogmatically insist that it is the same thing. There are still two other ways to interpret this passage that could be equally valid.
A third possible way to understand this passage is to look at the Greek conjunction kai, (Strong's Number 2532, καί). kai can be translated as “and” but it can also mean “even.” In this view, the passage could be translated to say, “you must be born of water, even the Spirit.” This would be similar to point two above where being “born of water” means to be cleansed by the word. Only in this case, Jesus is identifying the Agent of the cleansing as the Holy Spirit.
While these three may all be valid understandings, I believe the most likely meaning is that “born of water” is simply a reference to the physical birth. Even today, the amniotic fluid is referred to as “water” and when we’re born, we’re quite literally “born out of water.” Let’s examine the context of the passage again.
Jesus said to Nicodemus, “Verily, verily, I say unto thee, Except a man be born again, he cannot see the kingdom of God.” (John 3:3). It seems obvious that the phrase, “born again” necessarily compares the second birth (the spiritual birth) with the first birth (the physical birth).
Nicodemus apparently made the connection but became confused, thinking Jesus was referring to a second physical birth. John 3:4, “Nicodemus saith unto him, How can a man be born when he is old? can he enter the second time into his mother's womb, and be born?”
Now read the next to statements together (John 3:5-6):
“Jesus answered, Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God. That which is born of the flesh is flesh; and that which is born of the Spirit is spirit.”
I believe the passage is clear but let me paraphrase: “A person must be born physically AND spiritually. (because) That which is born of the flesh is flesh and that which is born of the Spirit is spirit.”
Now, skip forward a little further, Nicodemus is still struggling with understanding the spiritual rebirth. Jesus makes the following statement (John 3:12), “If I have told you earthly things, and ye believe not, how shall ye believe, if I tell you of heavenly things?”
We see Jesus is again comparing spiritual truths to physical truths. Jesus often explained spiritual truths by comparing them to things we understand. Consider the number of times Jesus said, “The kingdom of heaven is like…” In this passage, Jesus is comparing the rebirth - the spiritual birth - to the physical birth.
“Born of water” referring to the physical birth also agrees nicely with 1 Peter 1:23, “Being born again, not of corruptible seed, but of incorruptible, by the word of God, which liveth and abideth for ever.” So we are first born of corruptible seed (the flesh) and then we are born again of incorruptible seed (the word of God via the Spirit).
I will let the reader decide for himself the meaning of the term. While it seems to me that “born of water” very clearly refers to the physical birth, I can also see that there are other possible ways to understand the term. Furthermore, I believe the “born of water means baptism” explanation is the least likely meaning.
Further reading: Acts 2:38: Repent and be Baptized for the Remission of Sins