I put gallon water jugs in the freezer prior to camping trips ( to serve as ice blocks for the cooler and for drinking water when they thaw.) The jugs bulge around the side a bit but remain intact.
I'd keep them in a plastic milk crate so they don't get knocked around or punctured. Replace them in 6 months because the plastic may become brittle from the temp extremes in the trunk.

The Red Cross recommends you rotate your water stock pile every 6 months anyway. I try to use the old stuff when we go camping and replace it when we get back. I also store several extra cases of the 12 and 16oz water bottles which we use every day (lunches, kids soccer practice, to keep on my desk,etc.). That way the stuff is never older than a couple months.

Brian