A water trough is a stone-made structure containing water, scattered through and around the Castle, that the player may use to refill the Ancient Chalice with. Upon releasing holy energy from the Crucifix, the water inside the trough changes it's color to light blue, becoming holy water.
You can refill your Chalice as many times as you need, as the water in the trough never runs out.
While it's easy to acquire the Ancient Challice very early as one of the first rescue rewards (since Dr. Amersfield, and hence also Father Aville, are the easiest, and almost always the first hostages to be rescued), the entire East Wing section of the game is completely devoid of water troughs, meaning that you can only use holy water sparingly at that point - the only water trough you have access to at that point is the one in the Main Courtyard, in front of Main Castle entrance. It's not until you reach the West Wing until they start being commonly encountered, which is immensely helpful in dealing with much more powerful monsters encountered within.