There are two sides to a natural pool. One, naturally, is the pool. The other exists to clean the pool, naturally.
It starts off like most any other pool, scraping away thousands of dollars of sod and creating a hole that starts shallow and slopes deep. It has skimmers and returns. Auto water filler and LED lights. The only tell-tale sign that something's different, is the two-foot low wall along one side and the sloping cut section off to the side.

All formed up and ready for plaster at this point. The perforated return lines in the regeneration zone are a key to circulating clean water (courtesy of the plants above them) and turning the total water volume over three times in a twenty-four hour period.
Once the plaster is applied, water has to go in. A massive foot-wide cedar beam caps the low wall and remains completely submerged. The regeneration zone, loaded with gravel and a decorative assortment of boulders and new plants, literally and figuratively, comes to life. The whole project, to this stage, was completed over three months.
I'm curious at how the water flows, are you pulling from under the plant zone and pushing back to the swimming area?