Caistor was a Roman stronghold and takes its name from the Latin castra, meaning camp.
Part of the Roman wall can be seen on the south side of the churchyard, external, while a Roman cemetery was found during work on a supermarket development in 2010.
The building where the well was uncovered dates back to Georgian times and incorporates some Victorian structures.
It is being renovated to provide retail and meeting spaces, as well as holiday accommodation, as part of a “heritage hub”.
The trust, which is community owned, is looking to raise an additional £25,000 towards the £4.4m cost of bringing the building back to life.
Work is expected to be completed by the end of summer.