"Stagnant water" means water which is not flowing, like the water in a pond or a tank. When urination is prohibited at such places, defecating would be more sternly prohibited. One must also avoid throwing filth in it.
How vast and comprehensive the injunctions of Islam are, and how thoroughly Islam has grasped the problems of people, is something unique in the realm of religion. No other world religion can match it in this respect. It is very unfortunate indeed that in spite of having such perfect and complete religion, the Muslims are far away from practising its noble teachings. May Allah enable us to become true followers of Islam.