On April 4, 1760, Haines married Margaret Wistar (1729–1793), daughter of the wealthy glass-maker Caspar Wistar. They had five children:
1. Catherine Haines (1761–1808), who married Richard Hartshorne
2. Caspar Wistar Haines (1762–1803), who married Hannah Marshall and inherited the Wyck House estate. They were the parents of Reuben Haines III, scientist and farmer.
3. Josiah Haines (1764–?), who married Susan Harriett Bull
4. Reuben Haines Jr. (1765–1793)
5. Martha Haines (1769–1781)