They aren't eliminated they are just reduced to an acceptable level. The treatment plant looks at how much bacteria there are in the water and reduces them to a percentage where it would take say 30days for the survivors to increase to a level that exceeds their specifications (which still isn't necessarily dangerous) if they think that it takes less than 30 days for the water in their pipes to reach the consumer and be used - it is safe.

The bacteria load in stored water will depend on the number of bacteria left after the treatment process, the temperature (which affects their reproduction rate) the level of nutrients in the water (for them to feed on) and any toxins (either from the original treatment or that you have added).

The most likely source of bacteria in stored water is contamination from you handling and filling it.