According to Nicholas E. Denysenko in his book, The Blessing of Waters and Epiphany, it is in the 4th Century that we first see references in the Patristic authors to the practice of blessing waters.
“John Chrysostom, in his homily De Baptismo Christi preached in Antioch in AD 387, testifies to the practice of drawing sanctified water:
‘For this is the day on which he was baptized and sanctified the nature of the waters. Therefore also on this solemnity in the middle of the night all who are gathered, having drawn the water, set the liquid aside in their houses and preserve it throughout the year, for today the waters are sanctified.’” (Kindle Loc. 612-16)
However the first reference to the blessing of waters from texts dealing with liturgical rubrics comes from the 8th Century.
“The earliest occurrence of the ritual for the blessing of waters in the Eastern liturgical tradition is in the Euchologion Barberini 336 (BAR), which dates to the eighth century.” (Kindle Loc. 603-5)
Denysenko reports that the rubrics mention an order for the services which we have followed in our own parish when the Feast of Theophany falls on weekday:
“… beginning with the arrival at the Church at the ninth hour on January 6, immediately followed by Vespers and a Eucharistic liturgy. After the liturgy, the assembly departs for the blessing of waters…” (Kindle Loc. 694-97)
The 9th Hour is about 3pm. The services done were Vespers, the Divine Liturgy and then the blessing of water. One of the prayers listed for the service is the following beautiful prayer which recounts the deeds which God has done using water for the salvation of humankind:
You are our God, who in the days of Moses set free the Hebrew nation through the sea from the bondage of Pharaoh. (Exodus 14); You are our God who cleft the rock in the wilderness: the waters gushed out, the streams overflowed, and You satisfied Your thirsty people (Exodus 17);
You are our God Who by water and fire through Elijah brought back Israel from the error of Baal (2 Kings 10:18–28); Our God, who healed the bitter and barren waters by the salt of Elisha (2 Kings 2:19–22); Our God, who received the inseparable concord of the Trinity in the Jordan and who manifested the single paternal essence of your Godhead to us in it.” (Kindle Loc. 2572-79)