Police say the woman may have overdosed on drugs and been dumped into the water by someone trying to avoid being implicated in a murder.
Police have identified the victim as an African American woman and say she is from San Francisco. Her family says she had been missing for a few days.
The woman's name has not yet been released. Investigators broke the sad news to her daughter Wednesday.
Even though the medical examiner has not ruled this as a homicide, police are investigating the case as a murder. Investigators believe the suitcase was dumped around Folsom and Embarcadero, where it was found early Tuesday morning.
The Coast Guard assisted police by using a computer program that locates lost boats by looking at recent tide and wind data. By reversing the process, they can often tell where the boats came from.
The Coast Guard used the same program to find out where Laci Peterson's body was dumped. Her body was found at Point Isable Regional Shoreline in Richmond. Her husband Scott Peterson, who was convicted of the murder, said he had been fishing at the Berkeley Marina the day she was reported missing.
The program helped police link the two locations.
Margarito Real says his niece was the one who found the suitcase as they strolled down the Embarcadero.
"It popped open. It was like a second, like it flashed before my eyes," he said. "I saw a leg. I screamed. I said, 'I don't want to see that.'"