A sewer operations crew performing an annual inspection found the body at about 8:30 p.m. at the Embarcadero near Brannan Street, and immediately notified police, utilities commission spokesman Tony Winnicker said.
Police and fire crews waited until this morning's low tide to remove the body, Winnicker said.
Police spokeswoman Sgt. Lyn Tomioka said homicide investigators are investigating the death, which is considered suspicious.
It was not immediately known whether the body was that of a man or a woman, she said.
Winnicker declined to speculate on how the body might have gotten into the stormwater discharge box.
"They do have mechanical gates on them, so it would certainly be difficult," Winnicker said.
The commission maintains several of the large structures around the bay and ocean sides of the city, he said, to prevent sewer overflows onto the streets or into homes during major storms.