When a person is baptized is it the water itself that regenerates? Or is it the washing by the Holy Spirit that regenerates?
According to Calvin, and other Reformed commentators, the water in John 3:5 is not referring to water baptism. And it is the washing by the Holy Spirit that regenerates. And that alone.
We are seeing a lot of Reformed Christians who see themselves as High Sacramentalists influenced by Lutheranism, Anglicanism, Eastern Orthodox, Federal Vision, and certain Pre-Reformation theologians holding to the view that the water in John 3:5 is referring to water baptism. This view is predicated on poor handling of Scripture. Eisegesis is used to support the erroneous doctrine of baptismal regeneration.
We must always keep in remembrance the design of Christ, which we have already explained; namely, that he intended to exhort Nicodemus to newness of life, because he was not capable of receiving the Gospel, until he began to be a new man. It is, therefore, a simple statement, that we must be born again, in order that we may be the children of God, and that the Holy Spirit is the Author of this second birth. For while Nicodemus was dreaming of the regeneration (palingenesia) or transmigration taught by Pythagoras, who imagined that souls, after the death of their bodies, passed into other bodies,  Christ, in order to cure him of this error, added, by way of explanation, that it is not in a natural way that men are born a second time, and that it is not necessary for them to be clothed with a new body, but that they are born when they are renewed in mind and heart by the grace of the Spirit.
Accordingly, he employed the words Spirit and water to mean the same thing, and this ought not to be regarded as a harsh or forced interpretation; for it is a frequent and common way of speaking in Scripture, when the Spirit is mentioned, to add the word Water or Fire, expressing his power. We sometimes meet with the statement, that it is Christ who baptizeth with the Holy Ghost and with fire, (Matthew 3:11; Luke 3:16,) where fire means nothing different from the Spirit, but only shows what is his efficacy in us. As to the word water being placed first, it is of little consequence; or rather, this mode of speaking flows more naturally than the other, because the metaphor is followed by a plain and direct statement, as if Christ had said that no man is a son of God until he has been renewed by water, and that this water is the Spirit who cleanseth us anew and who, by spreading his energy over us, imparts to us the rigor of the heavenly life, though by nature we are utterly dry. And most properly does Christ, in order to reprove Nicodemus for his ignorance, employ a form of expression which is common in Scripture; for Nicodemus ought at length to have acknowledged, that what Christ had said was taken from the ordinary doctrine of the Prophets.
By water, therefore, is meant nothing more than the inward purification and invigoration which is produced by the Holy Spirit. Besides, it is not unusual to employ the word and instead of that is, when the latter clause is intended to explain the former. And the view which I have taken is supported by what follows; for when Christ immediately proceeds to assign the reason why we must be born again, without mentioning the water, he shows that the newness of life which he requires is produced by the Spirit alone; whence it follows, that water must not be separated from the SpiritCalvin’s Commentaries, John 3:5
It is quite clear that Jesus was not saying water baptism is salvific! Such a Romanist reading must be categorically rejected!
Water is often used in John as a picture of the Holy Spirit being poured out by Christ (John 1, 4, 7, etc.) in fulfillment of the prophecies like Ezekial 47. That is probably what he means here in John 3. Or it could refer to the waters which accompany childbirth, we all go through such waters when we are born. This verse is a favorite proof text of Catholic and Eastern Orthodox apologists.
Calvin further says in his Institutes:
25. Another passage which they [Romanists] adduce is from the third chapter of John, where our Saviour’s words seem to them to imply that a present regeneration is required in baptism, “Except a man be born of water, and of the Spirit, he cannot enter into the kingdom of God” (John 3:5). See, they say, how baptism is termed regeneration by the lips of our Lord himself, and on what pretext, therefore, with what consistency is baptism given to those who, it is perfectly obvious, are not at all capable of regeneration? First, they are in error in imagining that there is any mention of baptism in this passage, merely because the word water is used. Nicodemus, after our Saviour had explained to him the corruption of nature, and the necessity of being born again, kept dreaming of a corporeal birth, and hence our Saviour intimates the mode in which God regenerates us””viz. by water and the Spirit; in other words, by the Spirit, who, in irrigating and cleansing the souls of believers, operates in the manner of water. By “water and the Spirit,” therefore, I simply understand the Spirit, which is water. Nor is the expression new. It perfectly accords with that which is used in the third chapter of Matthew, “He that cometh after me is mightier than I;” “he shall baptise you with the Holy Ghost, and with fire” (Matt 3:11). Therefore, as to baptise with the Holy Spirit, and with fire, is to confer the Holy Spirit, who, in regeneration, has the office and nature of fire, so to be born again of water, and of the Spirit, is nothing else than to receive that power of the Spirit, which has the same effect on the soul that water has on the body. I know that a different interpretation is given, but I have no doubt that this is the genuine meaning, because our Saviour’s only purpose was to teach, that all who aspire to the kingdom of heaven must lay aside their own disposition. And yet were we disposed to imitate these men in their mode of cavilling, we might easily, after conceding what they wish, reply to them, that baptism is prior to faith and repentance, since, in this passage, our Saviour mentions it before the Spirit. This certainly must be understood of spiritual gifts, and if they follow baptism, I have gained all I contend for. But, cavilling aside, the simple interpretation to be adopted is that which I have given””viz. that no man, until renewed by living water, that is, by the Spirit, can enter the kingdom of God.John Calvin, Institutes, Book IV, Chap. 16
Here is what some other Reformed commentators have said about this passage:
First, The regenerating work of the Spirit is compared to water, v. 5. To be born again is to be born of water and of the Spirit, that is, of the Spirit working like water, as (Matt. iii. 11) with the Holy Ghost and with fire means with the Holy Ghost as with fire. 1. That which is primarily intended here is to show that the Spirit, in sanctifying a soul, (1.) Cleanses and purifies it as water, takes away its filth, by which it was unfit for the kingdom of God. It is the washing of regeneration, Tit. iii. 5. You are washed, 1 Cor. vi. 11. See Ezek. xxxvi. 25. (2.) Cools and refreshes it, as water does the hunted hart and the weary traveller. The Spirit is compared to water, ch. vii. 38, 39; Isa. xliv. 3. In the first creation, the fruits of heaven were born of water (Gen. i. 20), in allusion to which, perhaps, they that are born from above are said to be born of water. 2. It is probable that Christ had an eye to the ordinance of baptism, which John had used and he himself had begun to use, “You must be born again of the Spirit,” which regeneration by the Spirit should be signified by washing with water, as the visible sign of that spiritual grace: not that all they, and they only, that are baptized, are saved; but without that new birth which is wrought by the Spirit, and signified by baptism, none shall be looked upon as the protected privileged subjects of the kingdom of heaven. The Jews cannot partake of the benefits of the Messiah’s kingdom, they have so long looked for, unless they quit all expectations of being justified by the works of the law, and submit to the baptism of repentance, the great gospel duty, for the remission of sins, the great gospel privilege.Matthew Henry Commentary on the Whole Bible, John 3
By water then we are to understand the grace of the Holy Spirit in purifying the soul, which is fitly represented by the efficacy of water. And this purifying, refreshing virtue of the Spirit is promised in the prophecies that concern the times of the Messiah, under the mystical expression of water. Thus it is twofold by Isaiah, I will pour water upon him that is thirsty, and floods upon the dry ground, Isa 44:3. And this is immediately explained, I will pour my Spirit upon thy seed; and the Divine birth follows, they shall spring up as among the grass. In the same manner the effects of the Holy Spirit are expressed by Ezekiel: I will sprinkle clean water upon you, and ye shall be clean; and presently after, I will put my Spirit within you, Ezek 36:25,27. Our Saviour instructing a Pharisee, to whom the prophetical writings were known, expressly uses these two words, and in the same order as they are all set down there, first water, and then the Spirit, that the latter might interpret the former; for water and the Spirit, by a usual figure when two words are employed to signify the same thing, signify spiritual water, that is, his Divine grace in renewing the soul; as when the apostle says, in demonstration of the Spirit and of power, to signify the powerful Spirit. Thus John the Baptist foretold of Christ, that he should baptize with the Holy Ghost and fire, that is, with the Spirit, that has the force and efficacy of fire to refine us from our dross and corruptions. Thus our Saviour plainly instructs Nicodemus of the absolute necessity of an inward spiritual change and renovation, thereby showing the inefficacy of all the legal washings and sprinklings, that could not purify and make white one soul, which were of high valuation among the Jews. Entering into the kingdom of God, is of the same import and sense with the seeing the kingdom of God, in John 3:3: that is, without regeneration no man can truly be joined with the society of the church of God, nor partake of the celestial privileges and benefits belonging to it, here and hereafter.Matthew Poole’s Commentary, John 3
As you can see, all 3 Reformed commentators were in agreement that the water related to the work of the Holy Spirit. It is permissible to comprehend baptism on a secondary level because after all baptism does in fact represent cleansing from sin. But raising baptism to a level of operation as the sacramentalists do is making the passage say something it cannot bear. Christian baptism as a New Covenant sign will not be instituted by Jesus for perpetuity until the Great Commission, so one is hard-pressed to import baptismal efficacy into this passage. Baptism is a sign of the regenerating work already done in us by the Holy Spirit. Water baptism is in no way efficacious vis-a-vis salvation! It is done strictly out of obedience.
Advocates of baptismal regeneration typically have a four-part formula for how salvation is received. They believe that a person must believe, repent, confess, and be baptized in order to be saved. They believe this way because there are biblical passages that seem to indicate that each of these actions is necessary for salvation. For example, Romans 10:9–10 links salvation with confession. Acts 2:38 links salvation with repentance and baptism.
Repentance, understood biblically, is required for salvation. Repentance is a change of mind. Repentance, in relation to salvation, is changing your mind from rejection of Christ to acceptance of Christ. It is not a separate step from saving faith. Rather, it is an essential aspect of saving faith. One cannot receive Jesus Christ as Savior, by grace through faith, without a change of mind about who He is and what He did.
Confession, understood biblically, is a demonstration of faith. If a person has truly received Jesus Christ as Savior, proclaiming that faith to others will be a result. If a person is ashamed of Christ and/or ashamed of the message of the gospel, it is highly unlikely that the person has understood the gospel or experienced the salvation that Christ provides.
Baptism, understood biblically, is an identification with Christ. Christian baptism illustrates a believer’s identification with Christ’s death, burial, and resurrection (Romans 6:3–4). As with confession, if a person is unwilling to be baptized—unwilling to identify his/her life as being redeemed by Jesus Christ—that person has very likely not been made a new creation (2 Corinthians 5:17) through faith in Jesus Christ.
Those who contend for baptismal regeneration and/or this four-part formula for receiving salvation do not view these actions as meritorious works that earn salvation. Repenting, confessing, etc., do not make a person worthy of salvation. Rather, the official view is that faith, repentance, confession, and baptism are “works of obedience,” things a person must do before God grants salvation. While the standard Protestant understanding is that faith is the one thing God requires before salvation is granted, those of the baptismal regeneration persuasion believe that baptism—and, for some, repentance and confession—are additional things God requires before He grants salvation.
The problem with this viewpoint is that there are biblical passages that clearly and explicitly declare faith to be the only requirement for salvation. John 3:16, one of the most well-known verses in the Bible, states, “For God so loved the world that he gave his one and only Son, that whoever believes in him shall not perish but have eternal life.” In Acts 16:30, the Philippian jailer asks the apostle Paul, “What must I do to be saved?” If there was ever an opportunity for Paul to present a four-part formula, this was it. Paul’s response was simple: “Believe in the Lord Jesus Christ and you will be saved” (Acts 16:31). No baptism, no confession, just faith.
There are literally dozens of verses in the New Testament that attribute salvation to faith/belief with no other requirement mentioned in the context. If baptism, or anything else, is necessary for salvation, all of these verses are wrong, and the Bible contains errors and is therefore no longer worthy of our trust.
An exhaustive study of the New Testament on various requirements for salvation is not necessary. Receiving salvation is not a process or a multi-step formula. Salvation is a finished product, not a recipe. What must we do to be saved? Believe in the Lord Jesus Christ, and we will be saved.Got Questions? website, What is baptismal regeneration? article:
We are saved by grace alone, through faith alone. Water plays no part in our salvation. This is an essential and critical doctrine that has been obscured through the centuries until the Reformation.
The water certainly has no cleansing power whatsoever. The only reason why Peter could say that “baptism saves” (1 Peter 3:21) is because that is the point at which we are forgiven of sin based on the sacrifice of Christ. Hence, it is Christ’s blood—and only His blood—that cleanses sin (1 Peter 1:18-19; Revelation 1:5). [Recall that Peter clarified his “baptism saves” statement by adding “through the resurrection of Jesus Christ.” So baptism “now saves” via the atoning work of Christ, i.e., His death, burial, and resurrection—which is the Gospel (cf. 1 Corinthians 15:3-4).] The H2O of baptism is parallel to the water of the Jordan in 2 Kings 5. Naaman’s leprosy was not cleansed by those waters—but by God Himself the moment Naaman met the terms/conditions of cleansing (i.e., immersing 7 times). Similarly, the waters of the Pool of Siloam possessed no healing power. It was solely Jesus who restored sight to the blind man—on the condition that the man would go to that pool and apply the water to the mud Jesus had smeared on his eyes (John 9:7). Neither water nor mud, then or now, has any cleansing capability. They were merely mediums/conduits Jesus used to impart the blessing of physical cleansing to the blind man. The same may be said of the waters of baptism. God has always used physical conditions as preludes to His blessings, but the power remains within God’s own mind. Hence, salvation occurs in God’s mind the very moment a person complies with God’s stipulated condition(s). Water baptism is not the HOW of salvation—but, rather, the WHEN.
Regarding the “washing of regeneration and renewing of the Holy Spirit” (Titus 3:5) by allowing Scripture to interpret itself [see AP’s book Baptism & the Greek Made Simple, p. 142], it becomes apparent that the Holy Spirit regenerates people via His Gospel message which instructs the individual to be immersed in water. The term “Spirit” in John 3:5, 1 Corinthians 12:13, and Titus 3:5 all refer to the message (“word”—Ephesians 5:26) that the Holy Spirit provided via inspired writers/spokesmen. When that same message is presented to hearers today, requiring them to manifest faith, repentance, oral confession, and immersion in water (Romans 10:17; 2:4; 10:9-10; 6:3-4), and the individual complies with those prerequisites to salvation, when that individual rises from the water of baptism, he/she may then be said to have been regenerated by the Holy Spirit (i.e., based on the blood sacrifice of Christ, the Holy Spirit regenerated the individual by means of His stipulated prerequisites to cleansing by that blood). The Holy Spirit regenerates people via their obedience to the Gospel. Notice how Peter words it: “Since you have purified your souls in obeying the truth through the Spirit in sincere love of the brethren, love one another fervently with a pure heart, having been born again, not of corruptible seed but incorruptible, through the word of God which lives and abides forever” (1 Peter 1:22-23). “Through the Spirit” is a textual variant that may not have been in the original text, but it is nevertheless an accurate representation of the facts, since the only way for anyone to receive salvation from God is for Him to tell us how we may do so. God did so via the Gospel message authored by the Holy Spirit. When we read Scripture and implement its instructions in our lives, we are being influenced and instructed by the Spirit.Apologetics Press website, Does the Water Regenerate? article:
Thus we see that John 3 is not a proof text for baptismal regeneration. We must reject all aspects of sacramentalism whether it be Papist, Eastern Orthodox, Anglican, Federal Visionist, Lutheran, or other systems of faith. Sacramentalism is not the biblical means of salvation. Sacraments are a means of grace but only sanctifying graces, not the graces that belong to regeneration, remission of sins, or justification.
The Sacraments Do Not Confer GraceJohn Calvin, Consensus Tigurinus, Article 17
By this doctrine is overthrown that fiction of the sophists which teaches that the sacraments confer grace on all who do not interpose the obstacle of mortal sin. For besides that in the sacraments nothing is received except by faith, we must also hold that the grace of God is by no means so annexed to them that whoso receives the sign also gains possession of the thing. For the signs are administered alike to reprobate and elect, but the reality reaches the latter only.
Further, some Reformed Baptists and even Reformed have misinterpreted Calvin’s treatise on the sacraments to infer he supported baptismal regeneration, yet as we will see Calvin strongly and clearly argued against this doctrine in his Institutes.
This is from the second paragraph:
Peter also says that “baptism also doth now save us” (1 Peter 3:21). For he did not mean to intimate that our ablution and salvation are perfected by water, or that water possesses in itself the virtue of purifying, regenerating, and renewing; nor does he mean that it is the cause of salvation, but only that the knowledge and certainty of such gifts are perceived in this sacrament.John Calvin, Institutes, Book 4, Chapter 15
And this is from the fourth paragraph:
I know it is a common belief that forgiveness, which at our first regeneration we receive by baptism alone, is after baptism procured by means of penitence and the keys (see chap. 19 sec. 17). But those who entertain this fiction err from not considering that the power of the keys, of which they speak, so depends on baptism, that it ought not on any account to be separated from it. The sinner receives forgiveness by the ministry of the Church; in other words, not without the preaching of the gospel. And of what nature is this preaching? That we are washed from our sins by the blood of Christ. And what is the sign and evidence of that washing if it be not baptism? We see, then, that that forgiveness has reference to baptism.John Calvin, Institutes, Book 4, Chapter 15
THE HOLY SACRAMENTS
LORD’S DAY 25 Q & A 65
Q. It is through faith alone that we share in Christ and all his benefits: where then does that faith come from?
A. The Holy Spirit produces it in our hearts1 by the preaching of the holy gospel,2 and confirms it by the use of the holy sacraments.3