You know, thereās no reason why you couldnāt coat the interior with melted wax. Might be something to think about.
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You could line the compartments with heavy duty vapor barrier material and call it good. Fold and pleat, use spray adhesive to hold it in place if you feel the need.
Since youāre already familiar with XTC-3D, you know about Smooth-On. Check out their silicone rubbers. MoldMax Stroke is a brushable rubber that can hold a vertical face and would seal well in the corner joints too.
Or, try Smooth Cast 300 urethane resin. Mix, pour then slush it around in the compartment. It has a 3 minute working time so it goes very quickly and you can do multiple layers to build up thickness and durability.
Or, use a wood thatās native to tropic environments. Theyāre more resistant to rot.
For rounded corners you could laminate laser cut pieces. 
I have a Pegasus Touch stereolithography 3D printer that was primarily for smaller, more detailed items, and it does excel at those things. Larger simpler shapes however, Iāve found I can sculpt and shape them by hand in minutes using clay, cardboard and bondo, versus hours the printer takes and without the time invested in modeling a one-off part. Part of the motivation for me to purchase a GF is to have a mix of the two. Iāve noticed that a good percentage of items I would run on the Pegasus could actually be broken down into laminated materials plus a little touch-up by hand with fillers.
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Thatās a much better idea - your prints would print quickly and cheaply (as I said, solid infill is $$$$) and you wouldnāt have to worry about whether the plastic you have is waterproof.
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Oh, just remembered. There probably are sprayable sealants available at the hardware store, in spray cans. Or maybe even waterproofing/undercoating sprays at the local automotive parts store.
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Unfortunately, I feel like these carry the same risks as paint, since you wonāt know whether youāve sealed it improperly until it fails. I think the plastic sheeting is the best idea, since itās simple, cheap, and guaranteed effective.
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For something like this, with pretty much flat bottoms and vertical sides the 3D print would be pretty easy to get right (I would just break out the PET and the .75mm nozzle and do it in one shot) but compared to the time it takes to spray or brush on some lacquer or wax or poly itās not such a great use of timeā¦
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These are all great suggestionsā¦Iāll probably try several before deciding on which one works best.
(And I can easily add a false grid bottom with drainage holes inside the planter boxes too - I might do that with the larger pots - maybe just a half inch or soā¦put a liner in that section.)
Or just put holes in it. That might be easiest. (Donāt know, but Iām getting some good ideas.)
You could try coating them with plastidip, or perhaps spray them with Flex Seal if you trust itā¦
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thanks @Jules, if nothing else I had never heard of these little plants, no I think I want some, though my thumb is brown not green
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Since these are succulents (like cacti) they have a better chance with me as well. Chuckle!
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Have you considered Flex Seal (as seen on TV) for a liner? It comes in a spray and doesnāt seem to be that expensive. Iāve never used it, but itās been around for a few years so it would seem worth a quick try.
Anyone on the forums ever use it?
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Itās on the list to experiment with!
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Itās actually really good and seems to hold up for a long time
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It is pretty neat, would work great as a cool desk organizer. Pens, paper clips, etc etc.
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Yeah I was thinking variations on the theme would make great organizing for a lot of things.
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What if you made it out of clear acrylic with some various holes and an aquarium pump. It would be an interesting water fountainā¦ Maybe even plants in some of the boxes with the water fountain going down through othersā¦
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Ooooohhhhh!..Iād need to design a taller one to turn it into a water sculpture - maybe some different slanted angles for laminar flowā¦design for some curvesā¦how 2 hide the mechanism and hoseā¦
(Oh greatā¦triggered againā¦)
That would look pretty spectacular thoughā¦I need to get a bit better with Fusion first - itās taking me too long to make things happen now.
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Having constructed more RC model ships and boats than I can remember, my take would be to brush the inside of each container with fiberglass resin. If you want to go heavy duty, you could even use the lightest fiberglass cloth you could find, but I donāt think it would be needed. Substitute thinned epoxy if you donāt have fiberglass, as there will be no stress on the weakened formula.
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An easy to apply and generally available at Home Depot product called Red Gard is made to seal a drywall and tile shower stall or concrete wall or floor. It goes on like a very thick paint with a brush or roller. Totally water proof so you could use it with your Lithop planter or the future water sculpture. It will fill a gap 1/8 inch. Even tough it feel like rubber when it cures, mortar and adhesives will bond to it.
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Just make it out of frosted edge light acrylic and light it up with LEDs and have water flowing throughoutā¦
And maybe some soft music tooā¦lol
Go big or go home. 
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