I understand your want for a "pure" biological filter, I'm not a big fan of chemicals or other "additives" to any biological system.
I believe that depending upon the bioload of fish and frogs you use that you could easily achieve what you are thinking of doing.
Obviously the smaller the bioload the easier this is to create, and half the fun of creating vivaria is giving as much room as possible to the tankmates such that you can view a seminatural setup that might show off some natural behaviorisms of the inhabitants, my joy with my vivs is finding the inhabitants!
I think the easiest way to do what you are setting out to do would be to use a deep false bottom in a predrilled aquaurium with the drilling on the bottom using bulkheads, then simply set the height of your bulkhead such that you achieve your desired water level, and allow it to "surface skim" using a sump underneath with bioballs, or other media, and pumping the water back in however you want, perhaps creating a waterfall, or trickle wall, in this way by bringing the water back through the substrate in the vivarium you can offer the plants some great nutrients, and further biologically filter your water.
A great fish for a vivarium such as this would be something in the nothobranchius species, a killifish, they like shallow water, are fairly small, and if you are planning on keeping something like darts, the fish will take the same food source as the frogs
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Hope this helps, will be happy to repost to try and help you further, in the meantime yahoo has some groups that are all about this you can search for naturalistic vivariums in the yahoo groups, and you should come up with at least two that are wonderful.