Known problems exist with using soap, chemical solutions, or stimulants. For these just don't do it.
Water is more of a question mark now. Large enemas (several quarts) can wash the intestinal flora/fauna out enough to where you could have a problem (it's a balanced environment down there, where the good bugs help to hold the bad bugs in check), but small enemas shouldn't wash out enough to cause a problem.
What they don't know about yet is what happens to the rectal mucosa. They know that water can remove some of the top layer of the mucosa, but they're not sure what that means in practice (soap in the water removes much more). Isotonic water (with a little bit of salt or soda) and a PEG solution (also isotonic, so your body doesn't absorb it) didn't seem to have the same effect, but also didn't work as well.
There are some articles in a nursing magazine archive, but unfortunately I don't have access and don't have the spare cash right now to buy access to the whole story, so this is just based on the abstracts and the PD stuff.