Supposing you are actually sprinkling a little bit of the water (since by the rules, it is sufficient for you to have the components in a pouch)…
Any rpg where the rule simulate some kind of reality have to draw the line of what they simulate somewhere. In modern D&D, simulation of moment-to-moment adventurous tasks is generally more detailed than longer-term consequences of said actions. Downtime and crafting rules are at a far higher level of abstraction, for example. We could say that maintaining equipment is generally abstracted away into lifestyle maintenance cost.
Likewise, characters can swing a sword or cast a cantrip as often as they get turns (or more); however, the rules do not say how long the characters can keep this up. If a character tries to continue doing this for hours on with no rest and end, the game master and the group are fully within their rights to say that there are consequences, such getting fatigue. The abstraction of the game does not handle such scenarios.
It is best to discuss such issues openly among the group, so that everyone can buy in into the decisions and rulings made. Otherwise it might feel like someone, maybe the game master, is arbitrarily adding restrictions into the game.
The game rules suggest the game master makes such rulings without consulting the group, and this can be best in some situation (dramatic situation, immature group but mature game master, players who enjoy character immersion a lot, players whose fun is spoiled by both discussing the rules and trying to act optimally within them). The following quote is from the basic rules and is part of the fundamental structure of the game:
The DM narrates the results of the adventurers’
actions. Describing the results often leads to another
decision point, which brings the flow of the game right
back to step 1.
The game assumes that the spell components are not spent, and whatever wear and time and minor issues equipment might have, the characters fix during downtime, or replace their things every now and then, etc. We can assume that replacing the sprinklings of holy water is a part of this.
The level of abstraction assumed by the rules works well when the characters occasionally are in civilized regions, have a few hours of downtime every now and then, and are not utterly broke. These are not restrictive conditions and probably also hold in your game.
Maybe your character or party is like a Robinson Crusoe on his island, or in some other situation of great scarcity. Maybe they use a small amount of holy water every now and then.
In this situation, the implicit assumption of the characters maintaining their equipment, including the hard-to-get parts of it, is no longer valid. Hence, if the character use holy water every now and then and have no means of creating them, the game master or the group is fully within the rules to declare that they run out at some point. The players have declared their actions and the game master declares consequences.
Due to reasons of realism and player buy-in, it is advisable to mention that half the water is now used, and now there are only a sprinklings left, and so on.