Waterford's first goal came in unfortunate circumstances for the visiting side.
Bray keeper Evan Moran was subbed off after colliding with Blues' midfielder Sander Puri on 37 minutes.
The first task of replacement Mark O'Connor, was to scoop Puri's successful effort out of the net.
Noel Hunt had the ball in the net in the opening seconds of the second half, but was deemed offside.
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Hunt wouldn't be denied though and made it 2 - 0 on 72 minutes, turning quickly in the area after the Bray defense failed to deal with a Rory Feely cross.
It finished Waterford FC 2 Bray Wanderers 0.
Next up for the Blues is another home game on Friday against Sligo Rovers.
