There is a difference between a new sealed water bottle and a used water bottle. During the bottling process, the water and packaging are flash-pasteurized to kill most (hopefully all) bacteria. An open and used water bottle can be a breeding ground for bacteria - just like a stagnant pond in the summer time.
I commend you for wanting to reuse, either for "green" initiatives or simply to save some bucks. But, I would caution against it, especially for prolonged periods of time.
If you choose to reuse, I would recommend rinsing the bottle with warm soapy water EVERY day and possibly with bleach once a week. Please note, years ago, I attempted this for similar reasons. And even with washing every day, I eventually, and repeatedly ended up with a sore throat within a week or two.
What I currently practice at work is keeping a pint glass around that I fill with water from a fountain, filtered pitcher, or worst case, hot kettle water that I allow to cool.