Bertie married Philadelphia Norreys, daughter of Sir Edward Norreys, by whom he acquired the estate of Weston-on-the-Green. They had five children:

• James Bertie, married Elizabeth Harris and had a son, Norreys Bertie
• Charles-Montagu Bertie, rector of Uffington, died unmarried
• Eleanora Bertie, died unmarried
• Anne Bertie, died unmarried
• Catherine Bertie, married Francis Carr Clerke

In 1685, Captain Bertie led the troop of Oxfordshire militia horse during the Monmouth Rebellion. However, he lost his commission in November 1685 for failing to support in Parliament James II's installation of Roman Catholic officers. Subsequently, Bertie and his father-in-law Sir Edward Norreys went over to William of Orange on 25 November 1688. He was also a justice of the peace for Buckinghamshire.

After Philadelphia's death, Bertie married Catherine Fetherston (d. 8 February 1736), daughter of Sir Heneage Fetherston, 1st Baronet, but had no children by her. He died at Chesterton, Oxfordshire in 1734.

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