What does it mean to be "born of water" in John 3:5? John 3:5 (NKJV)
  
  Jesus answered, “Most assuredly, I say to you, unless one is born of
  water and the Spirit, he cannot enter the kingdom of God.


Does "born of water" means baptism i.e., water being used in that or Jesus mean something else?
There are two common interpretations of this phrase.  One is that &quot;born of water&quot; refers to baptism.  This view is typically held by those who adhere to baptismal regeneration.
The other view, which I will argue for here, is that it refers to actual physical birth.  In this view, the water might allude to amniotic fluid. This view seems far more likely to me as we view the passage in its context:

Jesus replied, “Very truly I tell you, no one can see the kingdom of God unless they are born again.”
“How can someone be born when they are old?” Nicodemus asked. “Surely they cannot enter a second time into their mother’s womb to be born!”
Jesus answered, “Very truly I tell you, no one can enter the kingdom of God unless they are born of water and the Spirit. Flesh gives birth to flesh, but the Spirit gives birth to spirit. You should not be surprised at my saying, ‘You must be born again.’ The wind blows wherever it pleases. You hear its sound, but you cannot tell where it comes from or where it is going. So it is with everyone born of the Spirit.” John 3:3-8 (NIV)

Notice that after Jesus says that we must be born of &quot;water and the Spirit&quot;, he immediately contrasts flesh and Spirit.  In the context, Jesus is answering Nicodemus's concern that he must be born &quot;again&quot;.  In one sentence, he mentions two births: water and Spirit.  And in the next sentence, he again mentions two births: flesh and Spirit.  The most natural interpretation is that flesh and water are referring to the same birth.
In addition, notice that Jesus says &quot;So it is with everyone born of the Spirit&quot;.  If he were intending to say that everyone must be born of flesh, water (baptism), and Spirit, then it seems that he would have said &quot;So it is with everyone born of water and of Spirit&quot;.  Water is painted here as the already accomplished (physical) birth.