Kunkel's first marriage was to singer Leah Kunkel, younger sister of Cass Elliot, and together they raised Elliot's daughter Owen, as well as having their own son Nathaniel, who is an Emmy Award-winning sound engineer.
Kunkel's second marriage was to singer Nicolette Larson (best known for her hit single, the Neil Young-penned "Lotta Love") in 1990 and they had a daughter.