The incident was reported at about 10:10 p.m., U.S. Coast Guard Petty Officer Dorian Jackson said.
A CHP helicopter responded to Sandy Beach in Vallejo to assist with a Coast Guard boat that had already arrived at the scene.
The victims' boat was sinking, and two people were injured on board, including a man with major facial injuries, according to the CHP.
The helicopter was asked to land at the scene by the Coast Guard because the area was not accessible by ambulance.
In the midst of high winds and a rising tide, the helicopter landed on the jetty and a paramedic walked to the boat, which was taking on about five gallons of water per minute, according to the CHP.
The male victim had suffered major injuries to his mouth and airway, and was removed from the boat with the assistance of the Vallejo Fire Department, which had arrived to assist with the rescue.
The man was lifted to the helicopter and flown to Queen of the Valley Medical Center in Napa to undergo emergency surgery, according to the CHP.
The female victim was walked to land and taken by ambulance to Sutter Solano Medical Center in Vallejo with minor injuries, according to the CHP.