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"This is He who came by water and blood Jesus Christ; not only by water, but by water and blood. And it is the Spirit who bears witness, because the Spirit is truth" (1 John 5:1-6). What exactly is St. John referring to? If Baptism, then whose baptism? Is it any reference to the Old Testament water rituals?

In reference to 1 John 5:6, our Lord Jesus Christ came through water, as the Holy Trinity was witnessed at the Lord's baptism; by blood, as His suffering was witnessed at His Crucifixion and death. The combination of water and blood were witnessed together as our Lord was hanged on the cross and  speared in His side, bringing forth water and blood. We, believers, obtain Salvation, through our faith, baptism, Holy Myron, confession and partaking of the Holy Eucharist, which is the Holy Body and Blood of our Lord Jesus Christ. This great mystery would not be available to us without baptism. 

In the Old Testament, the crossing through the Red Sea (Exodus 14) led by Moses and that through the Jordan River led by Joshua (Joshua 3), are significant events that point to baptism and a new beginning. The blood of the sacrifice is relevant from as far back as Abel (Genesis 4:4) and throughout the Holy Books of the Old Testament, as we are directed to the ultimate sacrifice, which was to come. The baptism of our Lord and affirmation that He is indeed the Christ, was proclaimed by the greatest of the prophets, St. John the Baptist, "Behold! The Lamb of God! who takes away the sin of the world!" (John 1:29).