A mikvah must consist of rain water which was never collected in a vessel beforehand. Mikvahs are, therefore, built with pipes which connect to the roof which funnel rain water directly into the mikvah pit. The water in the mikvah, however, must be changed quite often for hygienic purposes. And to wait every time the water is changed for there to be enough rain-water to fill the pit would be impractical because that could take sometimes weeks or even months.

A mikvah must consist of rain water which was never collected in a vessel beforehand... Mikvahs are, therefore, built with pipes which connect to the roof which funnel rain water directly into the mikvah pit... The water however, must be changed quite often for hygienic purposes

Therefore, we build a pit under the mikvah and fill it with pure rain-water. That pit is covered with a slat which has a small hole in it and the upper pit is filled with tap-water. The upper pit, which is where everyone immerses, can be changed as often as needed because the bottom pit, which is never changed because it is never used, remains pure rain-water.

While there are other solutions to this problem (have two pits beside each other), the bor-al-gabai-bor (pit-above-a-pit) system is the best one there is.