In 1679 Seignelay married twice; firstly to Marie Marguerite d'Alegre, who died in 1678. Secondly he married Catherine Thérèse de Goyon de Matignon Thorigny (1662–1699). Catherine was a daughter of Henri Goyon and Marie Françoise Le Tellier, herself a sister of François Michel Le Tellier de Louvois. Their four children included: * Marie Jean-Baptiste Colbert de Seignelay (known as Jean-Baptiste) (1683–1712) * Théodore Alexandre Colbert de Seignelay (known as Théodore) (1690?–1695?) He was succeeded as Navy Minister by the unfortunate Phélypeaux.