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I recently acquired a 125 gallon aquarium that I am going to use for my two turtles.
I would like to build a raised hood for it, but not sure if using wood or plastic is ideal.
Wood would absorb moisture and be have more potential to rot or mold.
I have never attempted to build something like this from plastic, so I am unclear as to what type of plastic to use, where it get it, and what materials or methods I can use.

Is plexiglass a suitable material? I am guessing that silicone sealant would be sufficient.

Most people use either egg crate or tile to support the bottom of the raided hood (usually called ATBA for above tank basking area). Wood can work provided its sealed and not in close contact with water. Glass can work but would be heavy and expensive. Plexi is great for the sides but a bit flexible for the base. Thicker/bigger pieces would be expensive as well. Silicone does not adhere well to Plexi.

Thanks, any suggestions for the type of sealant for the side inside if wood is used?

I don't know of a specific brand, but polyurethane is usually safe when fully cured. Some use epoxy though I've never tried it. Fish keeping forums would have a bit more info.