You might be able to seal it against contaminants somehow, I have heard you can put half a t-spoon of bleech per some amount of gallons and then it turns into salt in the water after it decontaminates it or something weird like that... I may be wrong so you should heavily research this as drinking bleach can cause death... If you could keep it pure then you woulnd't have to refill the containers
When I lived in Miami, I had a few sealed 5 gallon jugs that I used to store water for hurricane purposes. I also kept the empties around, and would fill them a day or two before the storm was supposed to hit.
The recently filled ones got used first, and were also the ones we used for washing dishes and cleaning. The "greywater" that was left over was poured into the back of the toilet to keep the toilet working without wasting potable water.
The idea was that we wouldn't tap into the sealed jugs for at least a week.