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I got a call the other day from a homeowner asking how to seal a toilet base to the floor. I think people believe that if the perimeter of the toilet isn’t sealed to the floor with something, then it will leak from under the base. That’s not true.
What seals the toilet base is the wax ring. The wax ring is soft enough to compress into any nook and cranny between the bottom of the bowl and the drain flange, yet firm enough to hold once it has been compressed. If the toilet leaks, it is likely that the bowl has moved and broken the bond.
I think a lot of “sealing” the bowl to the floor comes from appearance. People think if there is a gap then waste can leak out…and it can if there is a breach in the wax ring. If there is a breach in the wax ring, either the bolts weren’t tight enough, or one or both of them have corroded and broken, allowing the bowl to move.
If you are planning on filling this gap between the bowl and floor, most people simply caulk the gap. You can also use plaster of paris for this.
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