Are there any local or state regulations that you need to consider? In many locales, this would fall under Swimming Pool Construction and as such would probably mandate chemical sterilization at some level.
In the U.S., there are very few areas, that I am aware of, where a non-chemical swimming pool/pond is permitted.
If you construct this as a pond (never mentioning the word swimming), you may be able to get around it. Again, every region has different statutes.
Even if you can get around the authorities, if this pond is going to provide habitat to ANY vertebrate organism, the water WILL contain E. coli bacteria, of which most varieties are harmless, it is the few that are infectious that cause the most concern, and depending on location, the water may also contain fecal coliform bacteria, which is really your prime concern. There are also several other naturally occurring micro-organisms that can cause health problems in humans. I am not in any way trying to discourage you in pursuit of this project. Swim ponds have been in use in Europe and Southeast Asia for many years, apparently with little problems.
Several years ago, I did extensive research on Swim Ponds including eliciting an opinion from the CDC in Atlanta. Health-wise, they insisted that the only way to control and maintain a level of water sterility was through chemical means (read Chlorine). They did say, that on a residential site, a sufficient level of UV sterilization MIGHT be acceptable. This would require the installation of a commercial size sterilizer ($3.000 - $4,000).
As to the ultimate size of the phyto-filtration area, 40% of total surface area should do the trick. Flow rate through this filtration zone should be low to allow greater RT (resident time) for the plants to take up the nutrients and impurities.
Whether you will use bare liner with BDs or a backfilled lined pond determines a lot of the other decisions.
I assume that you are planning a Waterfall, hence the choice of a 20,000+ gph turnover rate. A low flow rate through the phyto-filtration can still be achieved with a simple wye and valve.
This may prove to be a lengthy thread as there are many factors that are peculiar to keeping a Swim Pond functional and balanced.
"Everybody is ignorant, only on different subjects." - Will Rogers