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Holy water is usually common tap water which has been magically transformed through the blessing of a priest. Holy water has the power to cure the sick and ward off vampires and demons. Oh, and it is a medieval melee weapon. When thrown on the ground, it creates a damaging flame that slides post-Rondo of Blood. A vial of holy water costs 25 gold coins.
In Christianity, holy water is usually associated with the Roman Catholic Church but it is sometimes used in other sects. Holy water is also found in other religions, including Hinduism, Sikhism, Buddhism, and Jainism.
It's also helpful for keeping your sinful infant from going to hell.
Roman Catholic holy water
Special blessed water has been important since early on in the Roman Catholic Church where it's a continuation of traditions from the Greco-Roman religion. Water can also be holy because of the place it comes from; you can even buy special holy water from Lourdes online, keep a bottle in your home or carry it with you and it will shield you from the powers of darkness. And since business remains profitable, the church won't complain.
Holy shit water
In spite of its supernatural properties, holy water becomes stagnant when kept in a container, and has the potential to spread bacterial and viral infections when people dip their hands into it on a continuous basis. This issue was possibly nullified when some Italians used technology to create and install a motion-sensing, hands-free holy water dispenser in one of their churches.
Studies have shown holy water may contain bacteria like Escherichia coli and Salmonella. A 2012 study found that only 14% of holy springs in Austria met biological and chemical standards for drinking water. The study also found that most of the holy water samples from churches and hospital chapels had high levels of fecal contamination indicators (holy shit!), coliform bacteria (76%), Escherichia coli (38%) and Enterococci (32%). How often this affects hospital patients with weak immune systems is unknown. 
- 2d4 damage per pint on impact, plus 1 splash damage with a 5 foot radius
- A Study of Primitive Elements in Roman Religion
- J.C. Rees and K.D. Allen, 1996 "Holy water—a risk factor for hospital-acquired infection". Journal of Hospital Infection 32(1), pages 51-55.
- Daily Telegraph (18 Sep 2013): Holy water 'unsafe to drink'.
- Reuters: Holy water at religious shrines and churches in Austria is often contaminated with fecal matter and bacteria (2013)
- Holy springs and holy water: underestimated sources of illness? by Alexander K. T. Kirschner et al. J. Water Health 2012 Sep;10(3):349-57. doi: 10.2166/wh.2012.005.
- "Holy Water May be Harmful to Your Health, Study Finds", Liz Fields, Sept. 14 2013, ABC