Permission to replace the block wood flooring with stone paving at the church in Charminster, Dorset, has been granted by the Diocese of Salisbury.
The upgrade will take place alongside continued work to replace a 16th Century village bridge blamed for causing the floods.
It is hoped work at the church will be completed within six months.
Church warden John Pearson said repairs to the church, which will also include fitting under floor heating, were expected to cost more than Â£100,000.
He said insurance, grants and fundraising would cover the cost, and added the church had already raised Â£35,000.
Gwen Yarker, who has lived next to the church for more than 30 years, described the flooding in January 2014 as "really very sudden".
She said: "The bridge acted as a dam and the river redirected itself through the churchyard and down the road.
"We had eight inches of river hammering against the house."
Authorities agreed the small arches of the Grade II listed, 16th Century bridge restricted the flow of the River Cerne.
English Heritage allowed it to be replaced with a bridge that has bigger arches.
Work started on the new bridge in May and is expected to end in October.
Some local residents and businesses had raised concerns about the five-month road closure.
Site manager Lorenzo Ferrari described the bridge works as "complex".
He said the old bridge had to be removed "stone-by-stone" due to its historic status.
"We'll be using some of the original bricks and stones to rebuild the bridge, as well as sourcing new Purbeck and Portland stone," he added.
Dorset County Council's chief engineer John Burridge said the new bridge "should reduce the frequency of flooding from once in every 10 years to once in every 50 years".
Work to repair a Grade I listed church hit by floods more than 18 months ago is set to begin.