Flushing dog poop down the toilet – without a bag, only the waste – is perhaps the best disposal method, says the U.S. Environmental Protection Agency and the National Resources Defense Council. Leaving pet waste on the ground increases public health risks by allowing harmful bacteria and nutrients to wash into storm drains, and eventually into local water bodies.
But cat feces should never be flushed, as it may contain Toxoplasma gondii, a parasite that can infect people and animals. Municipal water treatment systems do not always kill this parasite.
Leaving dog poop behind is good for the soil. Reality: In order for feces from a carnivorous animal to be used as an effective fertilizer, it has to be fully composted with other materials such as egg shells and grass clippings and allowed to break down over time.
Source: Pet MD