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There appears to be many origins to the surname Waters or spelling variant and this is very interesting as there appears to be many different haplogroups associated with the surname. 

Recorded in many spellings including Water, Wharter, Wauter, the diminutives Wattie, Watha, Wathey, patronymics Waters, Watheys, Watters, and the residentials Atwater and Attwater, this is an Anglo-Scottish surname of great antiquity. It has two possible origins. The first and perhaps surprisingly most likely origin, has nothing whatsoever to do with 'water'. It is a form of the male given name "Wauter", the medieval pronunciation of Walter, itself from the pre 7th century Old German name "Waldhar", meaning army-rule. This name was introduced into England by the Norman-French in 1066, and appears in the famous Domesday Book of 1086 as Walteri, whilst Waterus de Cantelupo was noted in the Danelaw for the county of Lincolnshire, in 1135. Early examples of the surname include: John Watter of Warwickshire, in 1214; Richard Wauters of Worcestershire, in 1275 and Ann Wathey at St Margarets Westminster, on November 23rd 1631, when she married Anthony James. The second possible origin is however residential and as Attwater describes somebody who lived by 'water'. This may have been locational as in the various villages called Water in the counties of Devon, Dorset, Hertfordshire, Lancashire, and others, or it may have described perhaps a place used for drinking water. Willim Atewatr appearing in the Curia Regis charters for Hertfordshire in 1198. John Waters, who embarked from London on the ship "Transport" bound for Virginia in July 1635, was one of the early settlers to the New England colonies of America. Throughout the centuries, surnames in every country have continued to "develop" often leading to astonishing variants of the original spelling.

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The name Waters in Ireland is derived from a number of native Gaelic Septs as well as being of immigrant origin, especially in the Province of Ulster. The O'hUisce Sept of Connaught and the O'Fuaruisce Sept of Donegal are two of the Septs that anglicized their name to Waters. Other variant names include Toorish, MacWatters and Watters.