Waterton is mentioned in the Domesday Book which records that, before the Norman Conquest, the manor was held by Fulcric who had one carucate of land with a hall. At the time of the Domesday survey, it was waste. It became the property of the Abbot of Selby and at some point between 1160 and 1179 when Gilbert de Ver was Abbot, it was given by him to Reiner de Normanby, son of Norman de Normanby, for an annual rent of twelve shillings, the payment of which is enacted annually at Luddington at Candlemas. Reiner took the name de Waterton. According to the 19th-century historian of the Isle of Axholme Rev Stonehouse: "this family is equal if not superior in a long line of ancestry to most of the commoners of England". Notable members of the family include John de Waterton (Master of the Horse), Robert Waterton (guardian of Richard of York, 3rd Duke of York), Sir Hugh Waterton, Sir Robert and Sir Thomas Waterton (High Sheriffs of Yorkshire), Lady Margaret Waterton (Lady of the Garter), and Charles Waterton the naturalist. Robert Waterton is mentioned in Shakespeare's Richard II.
Waterton became deserted in the late 15th or 16th century. Some excavation has been undertaken. It has now been taken over by the Strawson family. Only the seven-bedroom Waterton Hall remains, described by Pevsner as "a fine example of Georgian splendour".
- Folio: 369v Great Domesday Book
- "Lord of the Manor obeys order to pay: Lords of the Manor of Waterton should pay 12 shillings each year to the priest at Luddington." Lincolnshire Life vol 39 no 12 Mar 2000 p 7
- Rev W.B. Stonehouse, MA. The History and Topography of the Isle of Axholme, being that part of Lincolnshire which is West of the Trent, Longman, Rees, Orme (London 1839) p446
- J.W. Walker, OBE, FSA. The Burghs of Cambridgeshire and Yorkshire and the Watertons of Lincolnshire and Yorkshire (1931) The Yorkshire Archæological Journal XXX pp.314-419.
- William Shakespeare, "King Richard II" Act 2, Scene 1
- Carrott, J., Hall, A., Jaques, D., Kenward, H. and Large, F. An assessment of biological remains from excavations at Waterton, North Lincolnshire (site code: WGF96). (1996) Reports from the Environmental Archaeology Unit, York.
- R. Van de Noort & S. Ellis (Eds.), Wetland heritage of the Ancholme and lower Trent Valleys. An archaeological survey (1998), Hull: Humber Wetlands Project, University of Hull. ISBN 978-0-85958-193-6
- Beresford, Maurice & Hurst, John G., Deserted medieval villages: studies, London: Lutterworth Press, 1971
- Loughlin, Neil and Miller, Keith. A survey of archaeological sites in Humberside [Hull, Humberside]: Humberside Libraries and Amenities, c.1979[page needed]
- Pevsner, Nikolaus; Lincolnshire (Pevsner Buildings of England) (1989), New Haven, Connecticut, USA: Yale University Press ISBN 978-0-300-09620-0[page needed]
- "Origins in Lincolnshire - Normanby and Waterton Hall", Overtown Miscellany, Overtown.org.uk, United Kingdom Individual registered web site. Retrieved 11 October 2013