The expression "born of water," we believe, in no way means baptism. The new birth is the Savior's theme; without which no man can see or enter into the kingdom of God. It was not yet come visibly—"not with observation"—but it was there among them, as God's new sphere of power and blessing. Flesh cannot even perceive this kingdom. Christ had not come to teach and improve the flesh, as Nicodemus seemed to think; but that man might be partaker of a divine nature which is imparted by the Spirit. No mere external rite admits to the kingdom. There must be a new nature or life suited to the new order of things. "And Jesus answered and said unto him, Verily, verily, I say unto thee, Except a man be born again, he cannot see the kingdom of God." Then the Lord shows Nicodemus the only way of entering into the kingdom. "Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God." Water is here used as the symbol of the cleansing and purifying power of the word of God; as in Peter, "seeing that ye have purified your souls in obeying the truth through the Spirit." Here, the truth is spoken of as the instrument, and the Spirit as the agent, in the new birth as he goes on to say, "Being born again not of corruptible seed, but of incorruptible, by the word of God." Two things are necessary—the word and the Spirit. (1 Peter 1:22, 23.)
The passage obviously means the application of the word of God in the power of the Spirit—operating in the heart, conscience, thoughts, and actions; and thereby bringing in a new life from God, in which we have His mind, and His thoughts about the kingdom. The following passages will make it still plainer. "Of his own will begat He us with the word of truth." (James 1:18.) "That He might sanctify and cleanse it with the washing of water by the word." (Eph. 5:26.) "Now ye are clean through the word which I have spoken unto you." (John 15:3.) Here we have the moral cleansing or purifying of the soul, by the application of the word through the Spirit which judges all things, and which works in us new thoughts and affections, suitable to the presence and glory of God.
As a question of interpretation, then, we see no allusion to baptism in John 3:5: baptism may set forth that which is conveyed by it, but baptism itself conveys nothing. On the other hand—according to the inspired commentaries in the Epistles—baptism is the sign of death, not of giving life, as the Fathers uniformly affirm. "Know ye not," says the apostle, "that so many of us as were baptized into Jesus Christ were baptized into his death? Therefore we are buried with him by baptism into death." (Rom. 6; Col. 2; 1 Peter 3) Besides it is perfectly plain that Nicodemus could not possibly have known anything of proper christian baptism, as it was not instituted by our Lord till after He arose from the dead.