My water bottle strategy is three-fold:
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I store our water bottles in the fridge: the low temperature strongly inhibits fungal growth.
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And every once in a while we use baby bottle disinfectant to try and kill as much of the gunk that eventually starts growing in all the nooks and crannies.
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I replace water bottles after a year. In principle, I could get the top part separately for the bottles of choice (Camelbaks), but they cost almost as much as a new bottle. So I opt for replacing them outright. In fact, I have just received a shipment from wiggle with three new bottles, one for my wife and two for me. (My wife goes to the fitness studio three times a week, so she doesn’t need more than a bottle.)