Bourne Abbey Church has been temporarily closed to the public after flood water entered the building at the weekend.
The nearby Bourne Eau river flooded its banks on Sunday afternoon and water began entering the historic church soon after 1pm.
Lincolnshire Fire and Rescue Service was called to help pump water out and they were supported by volunteers with mops.
It is not yet known if the flood caused any long-term damage.
Father Chris Atkinson was at home in the vicarage when a neighbour knocked on his door to alert him to the situation at 1.20pm.
He said: “The Eau had backed up – a drain was blocked and the water came over the road and into the church.
“Sadly, being so close to the river, it’s one of those things. We’ve had minor flooding before but not like this in my time here.
“The parquet flooring could be damaged, but we won’t know until the building has properly dried out.”
Around half of the building was affected – with the water entering the north side of the building. It was around three inches deep at its worst.
The heating has been on around the clock to try and speed up the drying process.
Father Chris added: “We had a lot of people in church in the morning for a confirmation service and it wasn’t long after they had all left that the flooding occurred.
“We were fortunate that it did not happen earlier.”
It is hoped the church will reopen tomorrow (Tuesday).