Waterproof or moisture resistant? There is a big difference. If something needs to be waterproof it's assumed that it will either be constantly submerged or subjected to water directly. If it needs to be moisture resistant it's assumed that it will occasionally be exposed to spray or moist conditions. Generally, most indoor tortoise enclosures probably need to be moisture resistant. If that is your situation than even a good quality alkyd enamel latex paint will do fine. All of my indoor enclosures are painted with (a primer) and two coats of semi-gloss alkyd enamel latex paint and they have only needed to be repainted once in the past 20 years. The finish has protected the wood well and held up for all those years despite constant spraying (twice daily) and several inches of semi-moist to moist substrates, overflowing water dishes and tortoise wastes.
If you need to go truly waterproof plastic is the way to go.
There is a can of rubber cement that is spray on and works really well so far that I have heard. or you could line the bottom of your terrarium with a tarp. just depends on what you have or plan to do