A few weeks ago, Al got shell rot for the first time. We went to the vet and he told me that the rot was fungal in nature, and he told me something interesting: that fungal shell rot can be caused by high water pH. I had never heard that before.
I went home and checked my water's pH and I was shocked: it was super-high! Dr. White said that the ideal pH for a healthy shell is around 6; my pH was above 8. I have been slowly adjusting the pH over the last several weeks. Apparently my water is very alkaline right out of the tap.
So if your turtle has shell rot, check your pH and adjust it if necessary. If your pH is high, Dr. White said that for small habitats, you can use peat (found at garden shops) inside a piece of pantyhose, tied shut... it acts like a teabag. Peat is acidic, so letting it sit in the water will release those acids and lower the pH of the water.

