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Here's pictures of the set up. The plants in there are some water sprite in the water and some devil's ivy in the back corner, I plan on keeping those.
You can see the build up on the filter and parts of the glass. It's not a huge issue other than seeing in. It doesn't seem to have an adverse affect on anything living in there. If I'm being completed honest my main beef with this is really just the hard water coupled with the filter there. It's ment to work in very shallow water, but the splashing is causing most of the buildup on the glass.

I'm currently thinking I could make something similar doable in the larger tank, just with smaller and shallower water section. There is a water pump in there buried under the land side (you can maybe see the blue silicone outflow tube on the slab of rock). Would that coupled with the hydroballs and stone make a filter of sorts?

I know some mold is going to happen, I just live in a basement and wanted to keep the possibility of less friendly molds getting a start. I personally haven't seen a problem with the mold in this set up yet, but my landlord (mother) is all too happy to remind me that mold loves moisture.
I don't suppose I'd need a heater in the water if I got nothing really living in there, do I? The temp can get a little cold in my room (about 60c) in the winter but nothing terrible.