All silicone is waterproof. What you need is aquarium grade silicone which is just pure silicone without all the mould and mildew inhibitors added. You can get this at pet stores but, it tends to be rather expensive there or you can research and buy it in standard tubes for a caulking gun. I believe GE makes an aquarium grade silicone and the 3 pack of 500ml is less expensive than a 200ml "toothpaste tube" at local pet stores here.
You could use plexiglass but, keep in mind it scratches very easily and is probably going to look rough in no time. Call a Glazier with a description of what you need (dimensions, thickness and glass type) and I bet you will be pleasantly surprised.








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