Many issues relating to water baptism could be discussed, but the most important issue is whether it can obtain eternal salvation. Does a person have to be baptized in water in order to have eternal life?
The word baptize means to dip or immerse. Immersion best fits the biblical evidence (John 3:23; Acts 8:36-39) and best pictures the spiritual immersion of the believer into Christ's body (Rom. 6:3-4). This spiritual baptism at the moment of belief invests the believer with new and eternal life. Water baptism, which can occur any time later, pictures that spiritual transaction which unites the believer with Christ in His death and resurrection. A baptized believer publicly declares that he is a new person in Christ and now belongs to the body of Christ.
Jesus commanded that those who believe should be baptized and it is the expected norm for believers in the New Testament (Matt. 28:19; Acts 2:41; 8:12; 10:47-48; 16:14-15, 31-33). It is not presented as an option subject to one's preference, but neither is it ever given as a requirement for salvation.
The clearest statements of Scripture declare that eternal salvation is by grace through faith alone in Christ alone (John 3:16; 6:47; Eph. 2:8-9). Since grace means a free undeserved gift, any act or commitment intended to merit salvation is necessarily excluded (Rom. 11:6). Faith is the persuasion that God's promise is true, therefore it also excludes any deed or commitment because it simply accepts what has already been promised and paid for (Rom. 3:24; Eph. 2:8-9). When we say that our faith is in Christ alone, we mean that Christ did all that was necessary to accomplish our salvation and we can add nothing - no commitment, no act of obedience, no good work - to gain our salvation. We should therefore understand controversial passages on baptism in light of the clear scriptural teaching that faith alone in Christ alone obtains eternal life.
John's baptism. John the Baptist came to baptize unto repentance (Matt. 3:11; Mark 1:4; Luke 3:3). His baptism called the Jewish people to prepare themselves for the coming Messiah by repenting of their sins and their associations with apostate Judaism. That his baptism was not unto salvation is clear from Acts 19:1-5 where his disciples were told that they had to believe in Jesus Christ to receive the Holy Spirit.
Mark 16:15-16. It is disputed whether the end of Mark (16:9ff.) was in the original New Testament. Assuming it for the sake of argument, Jesus commands the disciples to preach the gospel saying, "He who believes and is baptized will be saved." But He then makes the only condition of condemnation "he who does not believe" (v. 15), not "he who does not believe and get baptized." Baptism is not a condition for salvation or condemnation.
John 3:5. There are a number of interpretive options for the meaning of "born of water and of the Spirit," but if the context is considered, baptism is certainly not the best. Some take water as a reference to physical birth, since that is what Nicodemus asked about (v. 4). It may be better to take water as a reference to the Holy Spirit ("water, even the Spirit" or "water, that is, the Spirit") since spiritual birth is the focus of the ensuing discussion (vv. 6-8) and something that Nicodemus, as Israel's teacher, should have known was promised in the New Covenant (v. 10; cf. Eze. 36:25-27; Isa. 44:3; See also John 7:38-39; Titus 3:5).
Acts 2:38. Several interpretations of this difficult passage deny the necessity of baptism for eternal salvation. Perhaps the one most consistent with the text holds that these Jews had believed when they were convinced of Peter's message, as is clear from their grief and their question "what shall we do?" (2:37). Repentance and baptism was Peter's prescription urging these new Jewish believers to identify with the Christian community in order to escape the imminent judgment coming upon their sinful generation for crucifying Christ (v. 40). Forgiveness of this sin (not their eternal salvation) was conditioned on the repentance signified by their baptism. Their repentant baptism was also the condition for receiving of the Holy Spirit for these Jews in this transitional period. Later, Gentiles received the Spirit immediately upon believing in Christ (Acts 10:43-44; 15:7-9).
Romans 6:3-4. It is very clear in this passage that Paul is speaking of the act of Spirit baptism which places (immerses) all who believe into the body of Christ. This Spirit baptism was predicted by Christ (Matt. 3:11; Mark 1:8; Luke 3:16; John 1:33; Acts 1:5) and is essential to all believers (1 Cor. 12:13).
1 Peter 3:21. In light of verse 20 which states that Noah and his family were saved through water because they were in the ark, so also believers are figuratively saved through the water of baptism only because they are in the resurrected Christ. In the context, these believers who faced suffering can be saved from a guilty conscience, which would come from denying their faith, by pubically identifying with Christ through baptism (cf. v. 16).
Other arguments could be cited to show that baptism does not obtain eternal life: Paul didn't see baptism as part of the gospel, and with a few exceptions, he didn't make it part of his ministry (1 Cor. 1:14-17); The thief on the cross was guaranteed a place in paradise without baptism (Luke 23:40-43); Cornelius and his household received the Holy Spirit (and thus salvation) before their baptism (Acts 10:44-48). But the most crucial argument against baptism as a condition for salvation comes from the nature of God's grace which is the basis of eternal salvation. His grace is always free and unmerited and only obtained through faith in Jesus Christ.