On January 11, 1776, Rush married Julia Stockton (1759–1848), daughter of Richard Stockton, another signer of the Declaration of Independence, and his wife Annis Boudinot Stockton. They had 13 children, 9 of whom survived their first year: John, Ann Emily, Richard, Susannah (died as an infant), Elizabeth Graeme (died as an infant), Mary B, James, William (died as an infant), Benjamin (died as an infant), Richard, Julia, Samuel, and William. Richard later became a member of the cabinets of James Madison and James Monroe.