The Divine Language of the Holy Quran has its own principles which every reader has to take care of while reciting it. The Quranic verses contain various punctuation, some necessary stops and pause signs and others optional. Waqf means to stop in Arabic.
The rules come from the Sunnah and they have been recorded as places where the Prophet stopped, or definitely stopped or sometimes paused. Part of the reason is to be able to reflect and comprehend the verse.