Charlotte married firstly James Howard, with whom she had a daughter, Stuarta. In 1672 she married William Paston, later the second Earl of Yarmouth, a member of the Paston family, and had issue. Both William and his father were in high favour with the Stuarts.
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With her first husband, James Howard (d. 1669), Lady Charlotte had a daughter:
- Stuarta Werburge Howard (d. 1706); died unmarried
Charlotte FitzRoy had at least four more children by her second husband, William Paston, 2nd Earl of Yarmouth:
- Charles Paston, Lord Paston (29 May 1673 – 15 December 1718), of Oxnead Hall, Norfolk
- Lord Paston was married to Elizabeth Pitt and had a daughter, Hon. Elizabeth Paston.
- Lady Charlotte Paston (1675–1736)
- She married Thomas Herne of Haveringland Hall, Norfolk, and had a son, Paston Herne, whose illegitimate daughter Anne Herne married Sir Everard Buckworth (later Buckworth-Herne), 5th Baronet, and was the mother of Sir Buckworth Buckworth-Herne-Soame, 6th Baronet. Lady Charlotte was also married to a Major Weldron.
- Lady Rebecca Paston (14 January 1680/1681–1726)
- She married Sir John Holland, 2nd Baronet; had issue of at least three children.
- Hon. William Paston (1682–1711), a captain in the Royal Navy; died unmarried
- G.E. Cokayne; with Vicary Gibbs, H.A. Doubleday, Geoffrey H. White, Duncan Warrand and Lord Howard de Walden, editors, The Complete Peerage of England, Scotland, Ireland, Great Britain and the United Kingdom, Extant, Extinct or Dormant, new ed., 13 volumes in 14 (1910-1959; reprint in 6 volumes, Gloucester, U.K.: Alan Sutton Publishing, 2000), volume XI, page 655.
- David Hilliam, Monarchs, Murders and Mistresses, p. 239 ISBN 978-0752452357
- Alison Weir, Britain's Royal Families: The Complete Genealogy (London, U.K.: The Bodley Head, 1999), page 256.