The water spoken of in the text from Isaiah is a figurative reference to the Holy Spirit. He is described as flowing like a riveret. It points to what happened at the event of Pentecost. Other Old Testament passages that portray the Spirit of God as being poured out in the manner of water would include Proverbs 1:23 and Zechariah 12:10.
Thus, we are to understand the words of Christ in regard to being born from above as bringing into mind the outpouring of God's Spirit. To be born again is a reference to the human soul being regenerated through the supernatural indwelling of the Holy Spirit. Our hearts and minds must be purified before we can enter the kingdom of God.