The water in the bottom of an eggcrate flooring is filtered as it passes through the layers. If you don't allow the water to get deep enough to come up through the substrate then any stagnant water is not really in contact with your flooring, and then you can just siphon it out. I use a large fish tank siphon with a hand bulb suctioner. It works well.
I don't have any pics of me siphoning out the tank, but you can see the two trap door I created in the back and the two eggcrate and mesh hole covers. I only put plants in a pot in the corner so I can easily slide them forward to put the siphon down in the hole.





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