As is true of the second Christian sacrament, the Lord’s Supper, the sacrament of baptism signifies or points to several spiritual realities. Westminster Confession of Faith 28.1 helpfully lists several of these realities, and one of them is regeneration, or the new birth that the Holy Spirit grants to the elect.
Today’s passage is given in the confession as a prooftext for the connection between baptism and regeneration. This is interesting because in the context of Jesus’ original encounter with Nicodemus, from which the statement recorded in John 3:5 comes, our Savior was almost certainly not referring specifically to Christian baptism. After all, at the time Jesus spoke to Nicodemus, the Great Commission had not been given, and Jesus could hardly have expected him to think of Christian baptism if it had not yet been instituted. What our Lord did expect Nicodemus to know in his vocation as a teacher of Israel was the Hebrew Scriptures, or the Old Testament. There, in Ezekiel 36:25–27, we find a prophecy that God would sprinkle clean water on His people Israel and fill them with His Spirit and with new life after they experienced the metaphorical death of the Babylonian exile.
Were the Westminster divines, the authors of the Westminster Confession, wrong, then, to include John 3:5 as a prooftext connecting water baptism and regeneration? No, because while there is no direct reference to baptism in Jesus’ words to Nicodemus, Scripture does frequently connect water imagery with regeneration. Jesus uses water and Spirit to refer to regeneration in John 3:5, and many other texts allude to the image of “washing” in connection with regeneration (Eph. 5:26; Titus 3:5). Baptism is a washing with water, so if Scripture connects regeneration and water, we must ultimately see the water of baptism as pointing to the reality of spiritual renewal.
So, baptism tangibly confirms God’s promise to cleanse from sin and give new life to all whom He has appointed. In itself, the rite of baptism does not confer new life, but the sacramental union between baptism and regeneration means that ordinarily, no one is regenerated without also, at some point in his life, receiving the sacrament of baptism. When we struggle to believe that God has granted us new spiritual life we can remember our baptism and be encouraged that the Lord, who cannot break His promises, has regenerated all who believe in Christ alone for salvation.