For a few years he was very successful, and in 1992 he married superstar Whitney Houston. However, rumors of marital problems haunted the couple throughout their marriage, including one time he was arrested for striking her. Both Bobby and Whitney had drug problems; both went through rehab. They had one child, a daughter, Bobbi Kristina, born in 1993; Brown has three other children from prior relationships. Starting in 1993 he began to have troubles with the law, with arrests for obscenity, assault and battery. In 1995 he checked himself into the Betty Ford clinic citing drug and alcohol problems, but this rehab and others did not keep him from additional arrests for drunk driving, cocaine use, marijuana possession, and multiple parole violations. He spent more than two months in jail in 2000 after refusing a drug test. In 2000 or 2001 he was diagnosed with bipolar disorder.

In 2004 Bobby Brown gave an exclusive interview to Stone Phillips of Dateline NBC along with his mother, Carol. He told Phillips, "I bought property probably in every state I went to and forgot about it. You know? I would leave cars on the freeway, just because, say, let's see what happens to it." Speaking of a period a few years later, he said, "I would spend like, I'm talking, days to weeks just high. I mean, just high, I mean, just on coke. You know? Marijuana at the same time, alcohol. You know? I wasn't a type that was going to discriminate. You know?" He also told Phillips he was now depending on medications to deal with his mood swings instead of drugs and alcohol.

Also in 2004 Brown told Jamie Fowler of Sister 2 Sister Magazine that he had been diagnosed with ADD – Attention Deficit Disorder – as a child. He mentioned that where he grew up, drugs were everywhere and you could not "even walk outside your door without someone being in the hallway smoking weed or drinking wine" and that he was always seeking attention. He said he sought help from doctors because "I was trying to figure out why was I going through these different changes. I mean, I could be happy one moment and then the next minute I'm like angry. Totally. Full of fire and rage."

On September 8, 2006, Whitney Houston filed papers in a California court requesting a legal separation from Brown, citing irreconcilable differences.