John 3:5

Christ, in his answer, repeateth what he had said of the necessity of regeneration, and withal, cleareth the way of it for Nicodemus his information; Shewing that this birth was not natural, but spiritual, wrought by the Spirit whose working is like unto water cleansing filth. To understand this water of Baptisme will not agree with this place; for, this water doth certainly regenerate, but every one that is baptized is not certainly regenerate, as witnesse Simon Magus, Acts 8.13.23. and others. Further, this water is pressed as absolutely necessary to salvation; whereas men may go to heaven without baptisme, if it be not contemned; as of old the elect seed of Abraham who died in the wildernesse without circumcision, were saved, so the thief on the Crosse was saved without baptisme. Therefore as Matth. 3.11. the holy Ghost and fire signifie one thing, or the Spirit working like fire in purging drosse, so the water and Spirit signifieth the Spirit working like water. Hence it is that verse 6. he repeats onely the Spirit, as including all that is here signified by the water and Spirit. And this expressing of the Spirits working, under the name of water, is no unusual expression in the Old Testament, Isa 44.3. Ezek. 36.25. Doctrine 1. No apprehension of impossibility in the matter of regeneration, doth warrant men to shift the thoughts of the necessity of it, or to think that any lesse then regeneration will availe them to salvation; for, Christ notwithstanding Nicodemus his doubt; presseth it as necessary, and gravely interposeth his authority (whom Nicodemus acknowledged for a Teacher come from God) to perswade him of it, Verily, verily, I say unto thee, except a man be borne of water, he cannot into the kingdome of God. 2. As Christ is meek and tender unto such as bring their doubts and ignorance unto him (and therefore informeth Nicodemus) so, mens questioning of truth, and their propounding of doubts against it, is an occasion that Christ makes use of for clearing of truth yet more; for, he taketh occasion of Nicodemus his doubt, to clear the doctrine of regeneration. 3. Regeneration is wrought neither by the power of nature, nor by outward Ordinances onely and alone, but by the efficacy of the holy Spirit, who doth prevent the sinner, and blesse outward means to him, before he can be changed; for, a man is borne of the Spirit. 4. The Spirit in working this change of regeneration, worketh like water; for, as water cleanseth what is filthy, and makes it bright, so the Spirit doth apply the blood of Christ, for cleansing polluted nature, and renewing of it in true holinesse; as water cooleth and refresheth the thirsty and faint-hearted, so the benefits purchased by Christ being applyed by the Spirit, do refresh the fainting souls of sinners in the perplexities and pangs of the new birth, or afterward, Psal. 42.1. And, as water fructifieth the barren ground, so the Spirit maketh the regenerate man fruitful in every good word and work; Therefore is this birth described to be a mans being born of water and of the Spirit.