How can a mikvah be kosher if rain water flows through it?

Question

Rambam Hilchos Mikvaos 8 (8) says:

The following rules apply when there are three cavities in a wadi, the higher one and the lower one contain only 20 se'ah, the middle one contains 40 se'ah, and a current of rain water flows through the wadi. Although the current of water flows into the cavities and out of them, it does not join the cavities as one. Hence, only the middle one is acceptable for immersion. The rationale is that water that is flowing does not join mikveot unless it collects in one place.

Rambam is talking about the suitability of mikvaos (and not a spring) since he insists on 40 seah. On the other hand rain water is flowing through the mikvah. How can such a mikvah be kosher? I thought a mikva needed its water to be still as it says in (תורת כהנים, פרשתא ט, ג)

ת"ל "אך מעין" – המעין מטהר בזוחלים, והמקוה באישבורן.

How then can a mikvah be kosher if rain water flows through it?

Answer 1

As mentioned in the comments, the Mikva already has 40 seah and the running rain water is in addition to that so it won’t make it passul. I’ve searched for a direct source for this on this Rambam and found it in the חיבר לטהר who addresses this very question in klal 3:10 VS Vehenai where he gives a number of options:

1. It’s talking about a case where the rain is running alongside the boros and touching a little, not running inside.
2. The Rosh holds that once it has 40 seah running rain water wouldn’t passul anymore.
3. The Shach says that if there’s 40 seah running water is only a problem if the water is running because of an internet problem of itself (I.e. a leak) but if the running is caused by an outside force, since there’s already 40 seah that wouldn’t be an issue even according to those who disagree with the Rosh