It is narrated from Sayyiduna Abu Hurairah, may Allah be pleased with him, that the Messenger of Allah, peace and blessings be upon him, said: "None of you should urinate in stagnant water and then perform ablution with it."
In this hadith, there is an instruction not to urinate in stagnant water, and the chapter concerns performing ablution (wudu) with such water. The reconciliation is that if someone urinates in stagnant water, then it is not permissible to perform ablution with it, as is made clear from «ثُمَّيَغْتَسِلُفِيْهِ». That is, a person may be in need of this water for drinking, ablution, or ritual bath (ghusl), but when it has been rendered impure by urine, such water cannot be used. And Allah knows best.