Haines married Jane Bowne (1792–1843) in New York on May 12, 1812. They had nine children:
1. Sarah Minturn Haines (b. March 30, 1812)
2. Margaret Haines
3. Elizabeth Bowne Haines (1817–1891)
4. John Smith Haines (1820–1850)
5. Hannah Haines (1822–1882)
6. Sarah Haines, who died in childbirth
7. Robert Bowne (1827–1895)
8. Margaret "Meta" Haines (1830–1878)
9. Jane Reuben Haines (1832–1911), both after her father's death, master of Wyck until 1911.
