Use more permanent solutions to store the water. Most plastics in water bottles you buy are thin and meant to degrade quickly. Even only slight wear can cause cracks. Your car vibrates and shifts direction constantly, and this only speeds up the process even if they are well stowed.

I usually keep my gear in the hatch away from water. I rotate water in/out all the time. I'm never without at least 1L. If you want to stow something, maybe get the water boxes or a couple of Nalgenes and stow them so the weakest point is pointing up. And it never hurts to review your supplies more often than not, but at least once a year for sure. Any time you stow gear with fluids, make sure that the gear is waterpoofed as well. Sucks to learn the hard way. I did once after leaving a case of soda in the car in the fall. Froze during the night, popping all of the cans. Wouldn't have been so bad, but they were upside down. When it thawed in the morning I had a slushy gooey mess that was embedded in the carpeting. <img src="/images/graemlins/smile.gif" alt="" />

If you want to go cheap, I've found that some of the 2L pop bottles can hold up for a long time. They don't have "crumple" zones for compressing them and have a fairly solid nature because of the pressures they have to take. Much better than any water bottles I've seen.