Most aux batteries these days are the "sealed" variety (Gel, AGM, VRLA will all indicate a mostly sealed unit). These batteries can usually be submerged in water up to about a metre deep for short periods before they're in trouble - and even then, some batteries can stay there for longer or go deeper.
I dare say though that 1m is more than enough and I doubt you're considering a day-long stay.
It's prudent that if you're contemplating lots of deep crossings (particularly in salt water) that you consider a sealant for the terminals - there's a blue spray that I've been told the name of a dozen times and still don't remember it that you should use on the terminals once everything's tightened up.