The sheriff's office received a call at 1:07 p.m. reporting that someone was threatening to harm himself or police in the 600 block of Riverview Place on Bethel Island.
Deputies responded and attempted to negotiate with the man.
The man had a shotgun and pointed it at deputies several times while they were attempting to negotiate with him, Lee said.
At 2:43 p.m. a sheriff's deputy shot him, Lee said. As of 3 p.m., the man was still being treated at the scene.