Hillenburg's wife, Karen, is a chef who teaches at the New School of Cooking in Culver City, California. Hillenburg deems her to be the funniest person that he knows. The couple have a son named Clay (born c. 1998). Hillenburg formerly resided in Hollywood and in Pasadena, and now lives with his family in San Marino, California. His hobbies include surfing, snorkeling, scuba diving, and performing "noisy rock music" on his guitar. He would jam with his son who is a drummer which, according to Hillenburg, is "a great way to bond with each other." He also enjoys birdwatching at home, but says that he was always "an ocean freak".  According to his colleagues, Hillenburg is "a perfectionist workaholic". He is also known for his private nature. Julia Pistor, co-producer of The SpongeBob SquarePants Movie, noted that Hillenburg is "very shy". She went on to say, "He doesn't want people to know about his life or family. He's just a really funny, down-to-earth guy with a dry sense of humor who puts his family first and keeps us on our toes in keeping our corporate integrity." Hillenburg said about himself, "I make animation because I like to draw and create things. I have no real interest to be on camera or to be a celebrity. It's not that I don't like people, but I like having my privacy."  In March 2017, Hillenburg disclosed that he was diagnosed with amyotrophic lateral sclerosis (ALS), a terminal illness that affects and causes the death of neurons that control the brain and the spinal cord. He released a statement to the Variety magazine after his diagnosis, in which he affirmed that he would continue to work on SpongeBob SquarePants "for as long as [he is] able." He stated further, "My family and I are grateful for the outpouring of love and support. We ask that our sincere request for privacy be honored during this time." Hillenburg is currently in the early stages of the disease, according to a source close to him.

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