The complaints have not been resolved by the charity or FRSB staff to the satisfaction of the complainant, so will be considered at board level.
Pete Meacham, compliance manager for the FRSB, said it had already met WaterAid and concluded there was nothing wrong with the event.
"We don't think there's anything for them to address," he said. "But as a member of the public has requested their complaint be considered by the board, the board will now have 60 days to investigate."
The complaints by Andy Strangeway, who campaigns for outdoor access rights, concern the charity's 2011 Corbett Challenge, which involves walkers reaching the summit of all 312 peaks between 2,500 and 3,000 feet in England, Wales Scotland and Northern Ireland at a specific time in June.
In an email to the FRSB, Strangeway alleged that the charity was guilty of several breaches of the Institute of Fundraising's Outdoor UK Challenge Events including the Three Peaks Code of Practice. The complaints relate mainly to alleged failure to consult land managers and possible threats to wildlife.
Andrew Cook, director of fundraising and communications at WaterAid, said: "WaterAid is aware of Mr Strangeway's complaint, which has now moved to the FRSB's third and final stage. We await its decision."