How to separate water and land?

Silicone will not adhere to acrylic. You need to use a Weld-on solvent bonding agent. There are a ton of youtube 'how to' vids on how to bond acrylics. There are also underwater aquarium epoxy putties that can do the job well if you want to complete an installation in an established tank. However, the job won't appear as clean as using a Weld-on bonding agent.

For a temporary setup, just use a piece of glass or acrylic going from the back right corner to the front left corner. Use silicone sealer along the edges and bottom seams to form a gasket (gaskets go on the pressurized waterside). Islands are out unless you use terracotta pots with the bottoms sealed together. Drill holes or cut notches in the bottom pot to allow water to flow through and place media, plants, etc. in the top pot.
As I stated, silicone will not bond to acrylic. If the gasket fails and water gets into the media there's a risk of stagnant water developing. The out-gassing from the stagnant media will displace O2 and kill your herps.