Is it reasonable to charge a clean up fee if the dog I am boarding has a diarrhea accident?

I essentially agree with the others that you should not ask for any additional compensation for the cleanup or the bath. Since you've already told the owner what happened and what you had to do, I would hope the owner would give you a generous tip for not only the inconvenience but the extra service you performed in giving the dog a bath. A nice conscientious owner is going to acknowledge you went beyond. I just had a dog staying with me who had diarrhea every morning in the house (also peed). Initially I attributed it to nerves, being in a new location, but it never improved despite the dog seeming to have settled in nicely. It continued throughout the stay no matter how many times I took the dog out, thinking I could avoid having to clean up inside. But it never worked. Anyway, the owner felt so bad that she paid me extra for my trouble on pickup; this was a non-Rover dog.

Just leave it to the owner to do the right thing, especially if you want to keep the dog as client. Also, letting the owner know that you need to know if the dog is experiencing any issues so that you can deal with them appropriately. I've made white rice and boiled chicken for more than one of my guests when their tummies were upset.

I agree with Walt, it's just 'one of those things' when caring for dogs.

I would be more concerned about a client leaving an ill dog with you, and not telling you it was ill. Why is the dog ill? Is it contagious? Sometimes owners will fail to mention things they think might cause the sitter to back out. Not fair to the sitter of course, but it's always good to keep in mind, and possibly have a tactful discussion with this client about your policy on accepting ill dogs (whatever that policy may be).

Sorry for the bad incident but as you know stuff happens. If this is a regular daycare client I'd bath him with asking for compensation, just chalk it up to going the extra mile and providing excellent service.