Not using water of any kind causes pyramiding. It's being raised in a dry environment that makes a bumpy tortoise. If you think about it, basically all water comes from some sort of well. To answer your question more directly, no, using well water is not a cause.
We highly recommend here....1. daily shallow warm baths. 2. Shallow water dish big enough to crawl into and self soak. 3. High humidity environment coupled with no lower than 80f temps.
These three steps stop pyramiding. Old info out there said diet had to do with pyramiding but that's been debunked.