It's pretty clear in Jesus' case - it was once.
But this is not a detail I would get a lot of concern over if someone said "Hey I would like to be dipped 3 or 4 or 5 times during my baptism"
Biblically we have no idea, but historically Jewish ritual tevilah involved a full body immersion, this could be several times--2, 3, or even more. John's baptism of repentance was a form of this Jewish practice, and so in form it probably didn't look different from standard Jewish tevilah. Without a time machine the only information we have to go off is what is written historically, such as in the New Testament (though Josephus also mentions John the Baptist), and the general knowledge of Jewish ritual practice of the time. So we can only make educated guesses.
Claiming that John's baptism was single immersion is fundamentally unknowable. It could have been, or it could have involved several immersions.
The fact that the early Church's normative custom was three-fold immersion (in the name of the Father, Son, and the Holy Spirit) simply links the Christian Sacrament of Baptism with its historically Jewish context, and gives the number special Trinitarian significance as per Christ's injunction that we baptize in the three-fold name of the Holy Trinity.
We also know that the early Church wasn't legalistic about the mode of Baptism, as the Didache presents clear evidence of what is ideal, but does not belabor the necessity of all details. Immersion was normative (specifically three-fold immersion as mentioned above), but affusion (again, thrice, in the name of the Holy Trinity) is perfectly acceptable when and where full immersion may not be possible. This, also, has basis in historic Jewish practice, as some ritual washings in Judaism involved pouring water--so it isn't surprising that the early Church accepted various modes of Baptism as valid.
Single immersion is, of course, perfectly acceptable; but it isn't the necessary mode of Baptism. There are several things necessary for Baptism to be valid Baptism, but the specific mode of Baptism isn't one of them.
Since Baptism isn't a work we do for God, but rather a work of God done for us, it would be improper for us to place unnecessary obstacles where God gives free and open invitation. The baptismal font is open to all, because the call of Christ is for all. Where certain things have been said about the proper way of baptizing the point isn't to place unnecessary obstacles, but rather to insist on a proper articulation of the Christian faith. Christian Baptism is Christian Baptism because it is Christian; and what makes it Christian is, according to the historic understanding of the Christian Church, that it is instituted by Jesus Christ, for the forgiveness of sins (not repentance, John's baptism was a baptism of repentance, Christian Baptism is for remission of sins by our dying, being buried with, and rising with Christ, this is by grace alone, not by our works), and we also insist that we use Christ's own words, "in the name of the Father, Son, and the Holy Spirit" to be explicit in our faith.
Even a heretic or an unbeliever could, in theory, baptize someone as a Christian; because what makes Christian Baptism Christian isn't about who administers the Sacrament; but that it is done in the Christian manner.
This is why the historic Christian Church has never been legalistic about the Sacrament of Baptism, and when people have tried to bring in legalism concerning the Sacrament the Church has responded by condemning such things as errant and heretical. For example, the Donatists were condemned as heretical because they tried to use Christ's Sacraments as a cudgel to punish, rather than to reconcile. God's grace is free and abundant, the Church has God's sacred command to be the instrument of Jesus in the world through which that grace is poured out: By the preaching of the Gospel and the administering of the Sacraments.
Legalism always kills,
Grace always gives life.
-CryptoLutheran