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?