Craig Walsh had a great chance to put the home side in front on 43 minutes, but lost control of a Dan McKenna pass in front of goal.
Walsh had another great effort saved saved in the opening minutes of the second half.
The Blues had chances of their own, Dean O'Halloran got on the end of a Derek Daly cross in the 80th minute, but shot directly at the Bray keeper.
It was Waterford's second draw at the Wicklow venue this season, and their almost 20 year wait for a win at the Carlisle Grounds continues.
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The Blues head into the mid-season break on 40 points, 7 ahead of Shamrock Rovers and Derry City.
