The surest way to ruin your distilled water is by storing it in a dirty bottle or container. This will introduce new bacteria or contaminants to your pure H2O.
The best way to ensure a clean container is to disinfect it using a natural product such as white vinegar. To make it even cleaner, you could use distilled white vinegar. Leave it in the container for a couple of minutes, then rinse it using distilled water.