Okay so to put things a bit clearer... The cleaning and maintenance of the setup would be accomplished as follows:
FW: 5-10% water changes every 2-4 weeks, using a Python siphon or similar. The water would be kept clean by a large external filter (or filter/sump combination) that would get it's media changed every two or three months (at most). The filter would have an incorporated heater so it wouldn't take up space in the water.
BW: Same as for FW but with more frequent water changes and very frequent top-ups with freshwater to keep salinity relatively constant (with a few seasonal fluctuations). Less filtration would be required for the brackish section due to mangrove plants being nitrate sponges and there being less biological load in that section.
Land: Millipedes, giant millipedes and wood lice would keep the substrate thoroughly turned over and tunnel through it a lot. Hermit crabs and land crabs would supplement this a bit when hiding an molting. Otherwise the land section would receive partial substrate changes (new coconut fiber, baking the sand) and spot cleaning for leftover foods and some waste. Waste cleaning on land is however not terribly necessary as most of the creatures would be fed vegetative matter (dried oak, almond and other leaves supplied readily, bark and wood "mulch", vegetables, some fruit-seasonal), and so their waste would go towards fertilizing the ferns, mosses and shrubs in the land area and old substrate could be used as compost in the garden. Of course the crabs would need "sea food" and tablets, flakes and sticks meant for omnivorous creatures (I would be very specific here and probably make my own-so many bad things are commonly used as preservatives in commercial foods for ie. hermit crabs).
The small SW section for the hermit crabs to soak in would just receie some basic water changes since nothing would be living in it permanently (to make things easier).
The whole thing would have moderate ventilation to allow clean air flow but keep humidity high. To answer a comment, of course the filters for FW and BW would be kept separate. I'm having second thoughts on the mudskippers... but Indian dwarf mudskippers wouldn't cause too much trouble.
Thanks for all the comments, I really appreciate the feedback so far and being a 16 year old aquarist with 9 years of experience in the hobby I think this idea is pretty good myself
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