Legend says that the religious settlement of "Ancarig" – the place of the anchorites – was founded in the seventh century by those looking for quiet and a contemplative life away from the temptations of towns. An article by a local historian, Avril Lumley Prior, is available here. After destruction by the Vikings and Saxon refoundation under the influence of St Aethelwold, a major Benedictine abbey developed. Models show the buildings of these times, and displays in the Museum describe the riches of the monks.

In the twelfth century, William of Malmesbury described Thorney as "a little paradise, delightsome as heaven itself may be deemed, fen-circled, yet rich in loftiest trees, where water meadows delight the eye with rich green, where streamlets glide unchecked through each field… And what of the glorious buildings, whose very size it is a wonder that the ground can support amid such marshes? A vast solitude is here the monk's lot, that they may the more closely cling to things above. If a woman is there seen, she is counted a monster,
but strangers, if men, are greeted as angels unawares. Yet there none speaketh, save for the moment;
all is holy silence."

The Benedictine Monastery was described, by some, as one of the largest in the land. But on the 1st of December 1539 it was surrendered at the Dissolution. Shortly afterwards it was ransacked by Henry VIII's forces. Much of the stonework was dismantled and sold to Cambridge to construct University buildings. Many samples of the carved stonework can be seen in gardens about Thorney. The Museum holds samples of the carved stone and masons means of identifying the worked stone with "mason's marks".

The land was granted to John, Baron Russell, in 1549. He became the 1st Earl of Bedford in 1550. This family then held Thorney for the next 350 years and were responsible for its development up to 1910.

The Norman, and later, abbey buildings have mostly gone, but much of the Nave survives to form the Parish Church of St Mary and St Botolph, also open to visitors.

Opposite the Abbey is a building called Abbey House. The front part is possibly the oldest building in Thorney and may have been built by the Duke of Bedford for his stewards from the sixteenth century.

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