Even if all you ever use is tap water they will eventually develop mold, not much you can do to stop it unless you use pure water and that would be pretty lousy to drink as it would lead to dilutional hyponatremia (water poisoning, pure water dilutes your body's electrolytes). Let's be honest, each time you bite the valve the bacteria from your mouth is introduced into the tube and if you fill from your regular drinking water source, this ain't a perfectly antiseptic environment from being splashed, touched and what-not.
Throughout the summer I keep the bladder full, bled of air (turn the bladder upside down and suck the air out) and in the fridge between uses rather than trying to drain and fill it every time, but I use it several days a week and so that can be a royal PITA. Plus your water is always cold. I usually only clean it a couple of times a year.
I clean them with a weak bleach solution. If the growth is bad I use a weak hypochloric acid (HOCl, Clorox bleach) solution. I use a full bladder (100 ounces in my case) of cold water with light capful (roughly 1/2-to-1 tablespoon) of bleach and let it sit overnight. Make sure no one drinks it, although it's weak enough solution that a sip is probably not toxic. If it's just a quick clean I use chlorine dioxide (ClO2, those drop-in purifier tablets you get from REI). These only take a few minutes and will blow up the bladder, so point the bite valve into the sink.
In both cases I rinse with 1 tablespoon of vinegar to neutralize. I mix the vinegar with a couple of cups of cold water and swish it around well, then a couple clean cold water flushes to get out the bleach and vinegar. I rinse with a baking soda & lemon juice dissolved in about a cup of warm water to remove the awful taste and usually will follow with a couple more warm water flushes.
Yeah, I only do this a couple of times a year. But the fridge thing makes it necessary only rarely.
'91 Pickup - Imelda
'08 Tacoma TRD - Donna