Technically , both rivers flow into Suisun Bay , which help flows through the Carquinez Strait to meet with the Napa River at the entrance to San Pablo Bay , which connects at its south end to San Francisco Bay , although the entire group of interconnected bays are often referred to as `` the San Francisco Bay . '' Technically , both rivers flow into Suisun Bay , which flows through the Carquinez Strait to meet with the Napa River at the entrance to San Pablo Bay , which connects at its south end to San Francisco Bay , although the entire group of interconnected bays is often referred to as â San Francisco Bayâ .