How do I replace the floor under the toilet that has dry rot?
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First be sure to fix the leak if it is the toilet it's self. It may be rotting because the toilet is not sitting completely flat and is leaking or breaking at the drain seal. You will need to remove toilet and if the wood is rotten it will have to be replaced BEFORE you redo the flooring and put a new toilet down. Otherwise the new seat may just fall through the floor with you on it. I have had the same problem and it was the sewer ring was uneven and I had to shim the floor level before putting the toilet back on, luckily the wood underneath was okay.
My first house had the same problem, had a guy tile the entire bathroom. He repaired the wood rot issue and then put about 1.5 inch morter down then tiled over that . lived there over 30 years, never had that problem again.
See if you don't find this helpful, Vicki:
http://homeguides.sfgate.com/repair-subfloor-under-leaky-toilet-83650.html
I've have done this. After removing the toilet I set my circular saw at about 7/8" to 1" depth of cut. I cut a square beyond the damaged wood around the toilet drain flange and pried it out. Replaced it with new wood.