Sounds like a cool idea and there is probably a way to do it... lined stream running through the bog and recirculating for the waterfall? Could look like it's part of the bog system but really be separate?

I have a bog that overflows to a pond with a waterfall to another pond. Plenty of leaks 'til I got some black, $16 a can, expanding foam sealant goo which seems to have worked (for now).

One thing I would NOT do is use perlite. It will float to the top.... I know, I know, you're going to top it with pea gravel, I still think it will work it's way to the top and make a mess. Why not use sand instead? My 2¢

Thanks. I actually think i have finally got my pond going so i wont be doing the waterfall bog....yet ;)