The song was mostly recorded during sessions for Badmotorfinger in 1991. In 2010, the band reworked the original recording with Down on the Upside co-producer Adam Kasper, who was working with the band on archival material. Cornell noted that when they listened to the original recording for the first time after almost two decades, he immediately remembered the problems he had with the song. Cornell explained that the original version of the song was much longer, and that he was unhappy with how it was arranged. He was also dissatisfied with the lyrics in the chorus. After so many years, however, Cornell noted that the issues seemed "easy to resolve". For the new mix, the music was re-arranged, the chorus vocals were re-written and re-recorded by Cornell, and new guitar overdubs were added. Kim Thayil explained to Rolling Stone, "[In] many ways, it's a new song."
The verse is notable for being in the time signature 9/8. In an interview with USA Today, Cornell noted that "Black Rain" captures "that super heavy version (of the band) we were finally realizing to its fullest potential about 1991."
The music video for the song, the first for Soundgarden in over a decade, premiered on AOL.com on September 20, 2010. It was directed by Brendon Small of Metalocalypse and is the first artist-driven music video to be based on the show. Virtual band Dethklok also make cameo appearances in the video.