I also fill it with hot water and 1/4 cup of bleach, then rinse with baking soda and water about every third or fourth ride.
Drew's got the answer. As little as a 10% bleach cleaning will keep your drink system clean. We use a lot of it for disinfection on the job. It is one of the cheapest and best disinfectants you can use- in small quantities.
It has been over 20 years since I drank from the streams. Any animal can carry giaridia. it is a nasty G.I. disease giving you fits of diarrhea. The only cure today is 'Flagil'. The cure is worse than the poison. If you must drink from a stream, at least carry the iodine and potassium tablets and follow directions for use.