you can get a complete drain assembly at any hardware store that will come with a gasket to prevent leaks
any construction grade material that you buy from home depot etc. that you want to waterproof with, is gonna have some sort of chemical in it that i don't recommend using. even the red pan that the guy was talking about before has chemicals that are used for fireproofing as well in it. any 2 part waterproofing is not recommended becuase of the chemical and catalytic reactions that happen.
what i can think of that is safe, is aquarium silicone. home depot sells plexi-glass in squares which you can cut and you can put those together and use aqaurium silicone and you will be fine as far as contaminents go. and the silicone will hold the plexiglass together no problem. no leaks.
primeing and painting will do nothing but cause a mess, eventually grow mold inside of the plywood once its soaked, and infect your water. marine board is super expensive and it is water RESISTENT not WATERPROOF.
I have used 8 mil plastic in a cardboard box that worked perfect to hold water.