According to the cheshbon in the machlokes Rav Sheshes and Rav Yosef it comes out that according to the Rabbonon, the mayim could check the Sota - and if she has a zechus - she won't die yet, but at the same time, she won't show any signs of 'detriment' (ie. so much so that we need eidim to posul her from eating terumah). Does she stay married for this time, or must she leave him out of sefeik? If the water checks her and she stays with him, how could the Mayim be machshil them to be together (since we say asur lebaal..)
Moshe, Jerusalem
Tosfos (6b, DH "v'Tehorah") says that it is apparent from the Bavli, and is clearly stated by the Yerushalmi, that the husband does not have to suspect that she has this special merit, and can be with her during this time.
Regarding your question, how could the Mayim be Machshil them to be together, let me first point out that the Mayim is not being Machshil her. She knows the truth, and whether or not she is forbidden (Rav Shlomo Zalman zt"l discusses in Minchas Shlomo vol. 3 whether she is obligated to run away in order not to be Machshil her husband).
Regarding the husband, the Mayim is something that works in a supernatural manner when Klal Yisrael deserves for it to be so. If a person is in this state and he does not realize that his wife is a "holy Sotah" who has a Zechus, there is probably a reason why Hash-m decided that this husband should be Nichshal, and it may have to do with him being Nichshal in similar areas in general. (For more on this topic, see 26b regarding Eishes Kohen and the Rambam in Hilchos Sotah 3:21).
All the best,
Yaakov Montrose