The victims have been identified as 39-year-old Michael Grace and 24-year-old Tayana Johnson.
Their families say they were in a dating relationship.
Someone called 911 around 4:15 a.m., reporting that two people appeared to be drowning after an argument.
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Grace was pulled out of the water by officers and later died at the hospital.
The Coast Guard and dive teams from Alameda County and San Francisco were called in to search the rest of the lake.
Divers later found Johnson's body after dragging the lake.
Investigators say she had signs of physical injuries.
Police say they are investigating Johnson's death as a homicide and the death of Grace as accidental.