The hydration layer makes this a lot easier than you think. Any flooding or leakage will just drain back into it. It is not a big problem, provided you have a good naturalistic substrate which is biologically active. The easiest solution would be to build a stream course that circulates the water in your hydration layer. You can do this with rock and gravel, and aquarium sealant.
First, build a filter you can remove and clean. You can do this with, say, wide diameter PVC pipe in two layers, a pump, a drill, and filter media of choice. Get a piece just wider than the pump, drill holes in it, then place a larger diameter piece (also with holes) around it, with filter media in the space between them.
place this in a hole in the false bottom. It will recirculate the water from the hydration layer (which presumably will have some biological filtration media like gravel or hydroballs).
Then you can build a waterfall. I would recommend using using cork bark (the natural pieces) siliconed together to form a box, or rock used the same way. You can then say, drill a hole to insert the tube for the pump, allowing the water to trickle down the channels in the cork (you will need to pick a good piece for this, or carve out a proper channel). This box can then simply be removed, and the filter media changed at will, and you can change the water using the pump. I suppose the waterfall could also be constructed using expandable foam.
A stream course can be constructed from rock siliconed together and sealed and then inserted into a trench in your primary substrate, draining into a clay dish (the type used with potted plants). They have a hole in the bottom that can be used along with a short length of aquarium tube as a drain back into your hydration layer (just cover the hole with screen to prevent clogging)





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