Nimor was married to Sandra Zober from 1954–1987 and to Susan Bay from 1989 until his death at age 83 due to complications of chronic obstructive pulmonary disease (COPD).
He was an LGBT ally. In 1991, he wrote a letter in support of increasing LGBT representation in the Star Trek franchise to the Los Angeles Times and also spoke out in support of Star Trek co-star George Takei's marriage to long-time partner Brad Altman and in opposition to California's Proposition 8, which sought to ban same-sex marriage in 2008, stating:
Absolutely NO on Prop 8 because I believe that gay people have every right to get married and share their lives. George and Brad have been together for many years. They have every right to be together in any way they choose. Prop 8 is completely unjust.