He married Anna Magdalena Smit in 1865, and the couple had three daughters (Anne Madeleine, Jacqueline E. van der Waals (nl), Johanna Diderica) and one son, the Physicist Johannes Diderik van der Waals, Jr. (nl) Jacqueline was a poet of some note. Van der Waals' nephew Peter van der Waals was a cabinet maker and a leading figure in the Sapperton, Gloucestershire school of the Arts and Crafts movement. The wife of Johannes van der Waals died of tuberculosis at 34 years old in 1881. After becoming a widower Van der Waals never remarried and was so shaken by the death of his wife that he did not publish anything for about a decade. He died in Amsterdam on March 8, 1923, one year after his daughter Jacqueline had died.