pond liner is a good idea, or you can look for commercial construction sites using rubber roofing (most) and score a few stray pieces for free.
EPDM pond liner and EPDM roofing is the same product, different color on top.
Shower pan liner from Home depot is the same product too BTW; just buy what you need and seal joints with a little contact cement.
Untreated wood is the ticket, seal either with clear or paint all edges to make waterproof.
If you are using paint, just get some laquer sanding sealer and apply, sand, then paint over it. If you stain, stain, sand, apply sanding sealer, then topcoat with clear.
Just get everywhere.