The body of a woman believed to be in her 40s was pulled from the water near the plane shortly after the crash. Two bodies were located inside the wreckage later Thursday afternoon.
The plane crashed at 11:53 a.m. According to the San Carlos Airport, two to three people may have been on board and the plane was en route to San Martin.
An employee of R.E. Borrmann's Steel Co. says the twin-engine Beechcraft Queen Air was owned by company founder 92-year-old Robert Borrmann.
Employee Charlene Marshall says Borrmann, his girlfriend and the pilot are believed to have been on the plane that crashed a mile after taking off from San Carlos airport.
The bodies insode the plane will not be removed until the wreckage is recovered.
The NTSB is headed to the scene to begin its investigation.
The Associated Press contributed to this report