It seems that Dracula’s dirt-bed must be consecrated (and originate from his native Transylvania), or to be “holy dirt,” so how can the addition of holy water make it utterly useless to the Count as a resting/rejuvenating spot?
Here are Van Helsing's words as he produces the consecrated host which he will use to render the boxes of soil uninhabitable for Dracula:
"And now, my friends, we have a duty here to do. We must sterilize this earth, so sacred of holy memories, that he has brought from a far distant land for such fell use. He has chosen this earth because it has been holy. Thus we defeat him with his own weapon, for we make it more holy still. It was sanctified to such use of man, now we sanctify it to God."
The soil is chosen for multiple purposes: it must be from the vampire's home country because they need a connection to their "home ground" (this is an invention from Stoker), and because that earth is drenched in all the blood that has been spilled on it throughout history.
Moreover, since it is (apparently) earth from a graveyard -- look at the phrase "because it has been holy" in the above quote -- this soil is the result of a desecration.
Stoker's Dracula is a representation of evil; in that context the opposite of that is represented by religious items like a crucifix or holy water, and such items can hold sway over vampires.
According to the book The Everything Vampire Book: From Vlad the Impaler to the vampire Lestat -- a history of vampires in Literature, Film, and Legend by Barbara Karg, Rick Sutherland, Arjean Spaite:
Stoker's use of the Eucharist speaks to a range of issues, including good versus evil, moral versus immoral, and dark versus light. No doubt the religious significance of the wafer is a religious reinforcement to the spiritual turmoil of the Victorian era. One possible reason that the wafers aren't as popularly used as holy water is likely due to accessibility. As a powerful representation of the body of Christ, wafers are typically locked away in tabernacles within churches and chapels and not easily acquired.