The goal is to eliminate long-term navigational and environmental hazards and prevent pollutants from entering the San Pablo Bay.
Participating agencies include the U.S. Environmental Protection Agency, the California Department of Resources Recycling and Recovery, or CalRecycle, the Sonoma County sheriff's marine unit and the Petaluma Police Department.
The EPA's emergency response program next week will start assessing the hazardous materials slated for removal.
CalRecycle will oversee the removal of the items from the river by a contractor in June, said Mark Oldfield, CalRecycle communications manager.
Abandoned vessels can contain oil, gas, diesel fuel, asbestos and lead paint, EPA spokeswoman Mary Simms said.
Law enforcement agencies can help determine who owns some of the vessels, Oldfield said. If the owners cannot be found, the boats will be considered abandoned and will be removed, he said.
The sites identified for cleanup stretch along the shore from state Highway 37 to the city of Petaluma.