Mahony, 23, suffered a broken leg and dislocated ankle during Ballygunner’s SHC victory over Ardmore yesterday and will miss the entire season.
Shanahan did not start for Lismore in their victory over Tallow but after coming on as sub, the 24-year-old aggravated a back problem and is facing a month on the sidelines.
Molumphy pulled a hamstring playing for Ballyduff against Mount Sion last Friday evening and as things stand, the 30-year-old former team captain is also out of the Semple Stadium clash.
This latest news compounds an already dire injury situation that has affected Waterford this season. Long-term injury victims Stephen Daniels and Brian O’Halloran have already been ruled out.
Jake Dillon, who recently underwent knee surgery, is rated as 50/50 to feature against the Rebels and Richie Foley recently suffered a fresh setback on the comeback trail following hip surgery.
2013 All-Ireland minor medallist Stephen Bennett is another concern as he continues rehabilitation on hip injuries.
Another former team captain, Shane O’Sullivan, is also ruled out through suspension after he was red-carded in the Allianz League relegation playoff against Dublin.