The earliest remains found in Thornton parish date to the Roman period. Roman pottery has been found by chance near Blackfields Farm and two Roman roads are known to pass through the parish. An excavation at Quabs Spinney uncovered a Roman corn-drying or malting oven and a possible wharf underneath, which may be even earlier than the Roman period, though this is uncertain.
It is known from documentary sources that there was a watermill in the village from the eleventh to the nineteenth centuries. St Michael's church is the oldest surviving building, having been built in the fourteenth century, though the north aisle was demolished in the seventeenth century and only rebuilt in the nineteenth. The church also lost its chancel in the eighteenth century during a period of restoration. There are historical records of chantry chapels being built in the fourteenth and fifteenth centuries, but these no longer survive. A fourteenth century stone effigy was found under the floor of the north aisle in restoration and a fifteenth century tomb and brass were restored to the church in the 1940s after a period of nearly two hundred years in the grotto at the convent. Medieval floor tiles had also been transferred to the eighteenth century garden grotto at the convent but are now at the County Museum.
The convent itself, though now an eighteenth and nineteenth century house, may incorporate parts of the earlier medieval building and medieval pottery has been found in the garden. Just to the south of the church once stood a parsonage, as recorded in the seventeenth century. An excavation in the 1970s uncovered the remains of a thirteenth to fourteenth century kitchen that could have, at one point, been part of the parsonage complex. There is a bridge just north of Thornborough parish that appears to have a fourteenth century core, though it has an eighteenth century casing. Part of the parish was imparked for deer in the sixteenth century and remains of the park pale in the form of a trackway can still be seen on the ground. It was disparked only in the nineteenth century. There are also historical records of the manor having a fishery from the sixteenth century and stone net-weights of that date have been found in the Ouse. Home Farm also had duck breeding and decoy ponds next to the Ouse in the eighteenth century and also a lime kiln and icehouse. The icehouse has survived in good condition. The nineteenth century formal gardens of the manor house can only be seen as parch-marks from the air.