In regards to the word "water" in John 3:5, there are those who would argue that the natural sense of the passage parallels water with being born out of a mother’s womb and with flesh based on the answer of Nicodemus to Jesus. Simply stated in that case, two births are necessary. The first is a physical, literal, "flesh" birth (which is, of course, accompanied by amniotic "water") and the second is Spirit.
There are also those who would argue that Jesus mentions "living water" in John 4:10, 14; 7:37-39 and in John 7:38-39, we read - "He who believes in Me, as the Scripture has said, out of his heart will flow rivers of living water. But this He spoke concerning the Spirit. The Holy Spirit is the source of living water and spiritual cleansing. If "water" is defined as baptism, then we could just as justifiably say, "Out of his heart will flow rivers of living baptism" in John 7:38. If this sounds ridiculous, it is no more so than the idea that water baptism is the source or the means of becoming born again. So to automatically read "baptism" into John 3:5 simply because it mentions "water" is unwarranted.
Yet there are still others who would argue that "water" is used in the Bible as an emblem of the Word of God, and in such uses it is associated with cleansing or washing. (John 15:3; Ephesians 5:26) When we are born again, the Holy Spirit begets new life and we are said to become "partakers of the divine nature" (2 Peter 1:4). The new birth is brought to pass through "incorruptible seed, by the Word of God, which lives and abides forever" (I Peter 1:23) and the Holy Spirit accomplishes the washing of regeneration. (Titus 3:5)