Holy Water is Aqua Pura unknowingly stolen from Megaton by the Church of the Apostles of the Holy Light (an offshoot of The Church of the Children of Atom) to which a large amount of "Atom's Light" (radiation) has been added in order to spread "the Glow of Atom's Light" to the "unenlightened." While The Church Of The Children Of Atom wish for Division (getting their atoms split), the Apostles Of The Holy Light wish to feel Atom's Glow (become irradiated). They believe that becoming a ghoul is humanity's next step towards perfection, and so "bless" Aqua Pura to help people achieve this holy state.
After Rosa gives holy water to Micky, she will give one bottle to the player. She has one more in her inventory. An additional one can be stolen from the beggar at this time, by picking his pocket after Rosa gives him the bottle but before he drinks it.
On first meeting Brother Gerard he will hand the player a bottle. He has two to four more bottles in inventory, which can be pickpocketed.
An infinite number can be obtained from Brother Gerard using an exploit. Drop all holy water and speak to him again, and he will hand over another bottle (this stops working after the first time the player drinks any, because that triggers the next step in Gerard's conversation script).