Having a reusable water bottle is an awesome idea for the environment, but it's also an awesome way to grow bacteria. Those critters love to hang out in wet places.
You wouldn't re-use a glass or a fork over and over again without washing it, so why do we re-fill our water bottles without cleaning them first?
Reusable water bottles should be thoroughly cleaned and dried between uses. Use one that has a wide mouth so you can get in there with a sponge or brush and plenty of dish soap and hot water.
The risk of bacterial and fungal growth are higher if you use the bottle with a drink that contains sugars like sport drinks or juices - so immediately rinse and wash the bottle after you're done.
I would hope it wouldn't get to this point, but if there is visible mold or slime in your water bottle, scrub that sucker and pop it in the dishwasher.
Fit's Tips: Get rid of your narrow mouth bottles - there's no way to clean them properly.