Abu Hurayrah (may Allah be pleased with him) reported that the Prophet (may Allah's peace and blessings be upon him) said: "No one of you should urinate in stagnant water then take a ritual bath with it." Another narration reads: "No one of you should take a ritual bath in stagnant water while being in the state of major ritual impurity."
The Prophet (may Allah's peace and blessings be upon him) prohibited Muslims from urinating in stagnant water, which is not running, because doing that would cause it to be polluted with impurities and microbes that the urine might be carrying. This, in turn, will harm those who use such water. In addition to that, the one who urinates in stagnant water may use it himself in taking a ritual bath. So, it is not logical to urinate in the water that he will, later on, use in purifying himself. Moreover, the Prophet (may Allah's peace and blessings be upon him) prohibited the one in the state of major ritual impurity from taking a ritual bath in stagnant water, because that causes the water to be polluted with the filth and impurities of the ritual state.