Take apart every part of the water bottle that you are able to and then follow the manufacturer's guidelines for washing.  Some water bottles are top-rack dishwasher safe, others need to be hand-washed.  If you have a water bottle with a straw, we recommend a straw brush as well to make sure you are able to get into small crevices.  After washing with warm water and soap or the dishwasher, the key is to let each piece fully dry before reassembling to avoid allowing mold to grow.