Klean Kanteen has a website that covers these methods - some of the suggested tactics work better than others. Check out the following methods and learn which ones work best.
Step 1: Take Me to Funky Town
juice and or coffee + hot car + time = FUNK
In the image below we left this insulated Klean Kanteen in the car for a few days with tea in it. When we opened it up there was mold everywhere growing on not only the tea bag, but the walls of the water bottle themselves.
Step 2: Wash With Bottle Brush
First up - wash the bottle using a bottle brush with hot water and soap.
The bottle brush physically removes the funk from the water bottle with scrubbing action.
Step 3: Wash in Dishwasher
If you've still got funk, read on.
Step 4: Overnight Boiling Water Soak
At the end of the soak, add soap, wash vigorously and reassess.
Step 5: Baking Soda and Water Soak
After the soak wash vigorously with soap and water and reassess.
Step 6: Overnight Vinegar Soak
Fill the water bottle with regular white vinegar and let it soak overnight.
(make sure you've removed all of the baking soda first otherwise you'll have a mini 2nd grade DIY volcano on your hands)
In the morning wash with soap and water. The bottle will have a slight vinegar odor for the first few minutes, but that will quickly dissipate and the water bottle should smell fresh and clean.
I'm sure that there are other methods to clean a funky water bottle. Leave comments with them and I'll test them out and upload them as additional steps to the Instructable in the future.
Good luck getting rid of the funk!