For long term storage, some people put them in the freezer so microorganisms can't grow.
That said, before every single game I play, I will run a cycle of boiling hot water through the bladder. I'll fill with boiling water, leave the bladder in the sink, squeeze the nozzle with my fingers, and suck on the end to get flow going (like siphoning gas) and then empty out the contents of the hot water through the bladder and the entire tube into a metal pot on the ground.
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SHÖCK
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