Water bladder "hydration systems" are very handy and amazingly tough. They puncture much more easily than a water bottle, plus have weak points for possible leaks where the tubing attachs and at the fill opening. A Nalgene can only leak from the cap, and while it is possible to puncture one, it would be very difficult. If a water bottle leaks, there are others that probably aren't leaking. If all the water is in one big bladder a leak could pose serious problems.

You don't want a weak bladder to take a leak on your back.

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