Dream Theater began to work on the album in October 2008. Mike Portnoy described Black Clouds & Silver Linings as, "a Dream Theater album with 'A Change of Seasons', 'Octavarium', 'Learning to Live', 'Pull Me Under' and 'The Glass Prison' all on one album."

The album's lyrics were written by John Petrucci and Mike Portnoy, and all except one concern personal experiences about disturbing or difficult moments of their lives. Though most songs were written by Petrucci, "A Nightmare to Remember" was based on a childhood car incident; "The Count of Tuscany" was about an actual encounter he had in Tuscany; and "Wither" was about the process of songwriting for him. "The Best of Times" was written by Mike Portnoy about his father, who died from cancer. "I just wanted to write something that was a tribute to our life together," said Portnoy, who played the song for his father prior to his death. "The Shattered Fortress" is the final part of Portnoy's Twelve-step Suite, reprising and concluding themes and motifs from the suite that began on 2002's Six Degrees of Inner Turbulence album. The remaining song, "A Rite of Passage", concerns Freemasonry; a video of the edited single was released on May 8, 2009.

"Wither" was released as a single on September 15, 2009. In addition to the album version of the song, the single contained an alternate version featuring only a piano and vocals, a demo version with John Petrucci on vocals, and a demo version of "The Best of Times” with Mike Portnoy on vocals. There was also a video to follow it which was released on November 18, 2009.