However, because you get standing water (that sounds a lot like my basement, by the way), consider adding casters, perhaps with rubber wheels, to raise the wood entirely off the floor. Or make rot strips with beveled edges that are thick enough to lift the bottom out of the danger zone. Chris wrote about this here: http://www.popularwoodworking.com/woodworking-blogs/chris-schwarz-blog/how-to-save-your-tool-chest-and-your-tools-from-water

I don’t think any finish is going to provide long-term protection against water – once you get one tiny scratch in that finish, the moisture will be through the barrier. But if you feel you have to finish the bottom, Bob Flexner writes that paint is the most effective coating to combat the elements (and oil-based wears better, according to his book “Understanding Wood Finishing”). The best clear finish for this purpose would be a marine varnish.

My chest is in an unfinished (rented) basement shop with unsealed concrete floor that gets some very shallow puddles if we get a lot of rain. The floor’s dry in a day or so, but since it’s also cool, I worry about condensation and encouraging mildew underneath something that’s close to the floor, even on something like cypress that’s naturally resistant. (Tung oil? Hoping for something that won’t require taking the chest outside to apply and maintain, but I’ll do it if I have to.)

Then, imagine wetting your brush with your carefully chosen and carefully mixed milk paint–for you are mixing two or three milk-paint colors to achieve a certain color you have chosen after a few days of consideration, because you don’t have time to dither–then drawing the brush across your freshly planed surfaces only to think, “Wow, that looks pretty wack.”