If this bothers you, you could borrow a ruling from an old DM of mine. In his world, holy water only remained holy as long as it was in its special flask or font. Once you did anything with it-- dumped it on a vampire, poured it into a barrel, absorbed it with Dust of Dryness-- it had its instantaneous effect (if applicable at that moment) and then immediately turned nonmagical.
This was the DM's way of shooting down a very annoying PC plan. Long story short: they wanted to flood an entire cavern complex with holy water, to a depth of several feet. They thought that'd be easier than going in and hunting the vampires by hand.