It’s best to clean the water bottle and any associated filtration systems after each use. That way bacteria and other microscopic organisms won’t have a chance to build up in the cracks and crevices of your water bottle.
How you clean the bottle depends greatly on what the bottle is comprised of. While it’s best to follow the manufacturer’s direction, for the most part, hand washing it with mild soap and water and allowing it to air dry before closing it will be more than enough. On occasion, there will be a water bottle that is dishwasher safe, but even then, it’s a good idea to inspect it after each washing for damage.