There are a lot of problems with using John 3:5 to support baptismal regeneration. I've written about those problems in many posts over the years. I'll briefly summarize some of the points I've made before, then move on to what I want to focus on in this post, verse 8.
Jesus' rebuke of Nicodemus for not understanding what he's saying (3:10) makes more sense if he's referring to something that can be more easily derived from the Old Testament than baptismal regeneration can be. He goes on to refer to justification through faith a few times (verses 15-18), without any reference to baptism, which also makes more sense if baptismal regeneration isn't involved. The other New Testament passage that uses the born again language, 1 Peter 1:23-25, associates that language with a response to preaching, which is a prebaptismal context. See my discussion of justification apart from baptism in 1 Peter here. For a discussion of how the preaching context of justification is problematic for baptismal regeneration, see my post on Galatians 3 here. In the timeframe after Jesus spoke to Nicodemus, the fourth gospel and the other gospels give us several examples of people being justified apart from baptism, including in contexts that seem to be normative rather than exceptional, and there aren't any examples of people being justified at the time of baptism. See my post here on the double healing phenomenon, for example. The evidence for justification apart from baptism in the gospels is such that advocates of baptismal regeneration frequently concede the point and claim that baptismal regeneration didn't go into effect until after the crucifixion or at some other later stage. That creates problems for their view of John 3:5, which uses the present tense and makes no suggestion that what Jesus is discussing wouldn't go into effect until later. There's also the fact that the evidence suggests continuity in how people were justified throughout history, not the sort of discontinuity baptismal regeneration involves. For more about that subject, go here. And contrary to what advocates of baptismal regeneration often claim, there wasn't universal or nearly universal agreement about their interpretation of John 3:5 prior to the Reformation. For discussions of the many interpretations of the passage that circulated before the Reformation, including some that are inconsistent with each other, see here, here, and here, among other relevant posts in our archives.
Most likely, what Jesus is doing in John 3 is drawing from some material in Ezekiel 36-37. Those chapters in Ezekiel refer to water, wind, and the work of the Holy Spirit in contexts that involve the bringing about of new life (being born again, as Jesus puts it; being made a new creature, as Paul puts it in 2 Corinthians 5:17; etc.). Ezekiel uses a lot of eschatological language and refers to a new covenant. In contrast to how baptism was typically practiced at the time when Jesus spoke to Nicodemus, Ezekiel refers to sprinkling with water (36:25). And he goes on to discuss wind in chapter 37, which Jesus discusses in John 3:8 (in the same order as Ezekiel: water, then wind). Most likely, then, the water of John 3:5 is summarizing one aspect of the Spirit's work, namely his cleansing, while the wind of 3:8 is summarizing another aspect of his work, its unpredictability. In addition to the close association of the water and the wind in both Ezekiel and John, the two are closely associated conceptually. They're both commonly experienced elements of nature. The wind obviously isn't literal in John 3. It would make more sense for the accompanying water to not be literal either. Furthermore, the unpredictability of the wind doesn't sit well with a highly visible ceremony that's anticipated ahead of time, like baptism. That's reminiscent of what we see elsewhere in scripture about the immediacy of justification, how it can happen at any moment (2 Corinthians 6:2) and by a means we have immediate access to (Romans 10:8-10). Baptism violates both of those kinds of immediacy, and it makes less sense of John 3:8.
