A priest said it was "incredible" that burglars would smash their way into his church and urinate in the holy water.
The act was noted by police after they were called on Thursday morning to the break-in at St Mary's Roman Catholic Church in Bridge Street, Sunderland.
Would-be thieves smashed a large window to get into the church, then used fire extinguishers to try to break down doors, before seemingly getting bored and leaving empty handed.
But not before someone urinated in the holy water stoup.
Father Marc Lyden-Smith said: "Our cleaning volunteers came in on Thursday morning and saw the damage.
"A police officer noticed there seemed to be urine in the holy water stoup.
"It is incredible.
"It has been cleaned out, of course."
Fr Lyden-Smith said the pope has called for people to show mercy.
"It is disappointing but it is the year of mercy and we have to keep that in our thoughts," the priest said.
Holy water is used by Catholics to make the sign of the cross when they come into church and the stoup or font is usually by the entrance.