Bearded dragons may get diarrhea from a number of causes such as stress, parasites, bacterial infections of the intestine, atadenovirus infections, spoiled food, malnutrition, dirty water bowls, unsanitary cages, and inappropriately cool or excessively high temperatures in the cage.
An extremely common parasite is coccidia, Isospora amphibolori. This can quickly be devastating to baby bearded dragons but adults seem to live well as long as they are kept under ideal conditions. Other parasites such as flagellated protozoans and amoebas are often found when fresh feces is examined under a microscope.
Amoeba found in the diarrhea of an adult bearded dragon.
Whenever you see your bearded dragon has diarrhea, collect a small sample of it in a plastic bag and bring it to a veterinarian to be checked for parasites. Start soaking your bearded dragon in shallow warm water for 15 minutes a day to make sure it has enough to drink. Double check that the cage temperatures are warm enough and that the ultraviolet-B bulb is working. If the diarrhea persists for more than 2 days, your bearded dragon needs a thorough examination and should be seen by a veterinarian as quickly as possible. Baby bearded dragons often get very weak quickly from diarrhea and should be evaluated right away rather than simply bringing in the fecal sample for an evaluation.