San Francisco Bay is one of the largest estuaries along the U.S. West Coast and is linked to the Pacific Ocean through the Golden Gate, a 100 m deep bedrock inlet. A coupled wave, flow and sediment transport model is used to quantify the sediment linkages between San Francisco Bay, the Golden Gate, and the adjacent open coast. Flow and sediment transport processes are investigated using an ensemble average of 24 climatologically derived wave cases and a 24.8 h representative tidal cycle. The model simulations show that within the inlet, flow and sediment transport is tidally dominated and driven by asymmetry of the ebb and flood tides. Peak ebb velocities exceed the peak flood velocities in the narrow Golden Gate channel as a result of flow convergence and acceleration. Persistent flow and sediment gyres at the headland tips are formed that limit sediment transfer from the ebb-tidal delta to the inlet and into the bay. The residual transport pattern in the inlet is dominated by a lateral segregation with a large ebb-dominant sediment transport (and flow) prevailing along the deeper north side of the Golden Gate channel, and smaller flood dominant transports along the shallow southern margin. The seaward edge of the ebb-tidal delta largely corresponds to the seaward extent of strong tidal flows. On the ebb-tidal delta, both waves and tidal forcing govern flow and sediment transport. Wave focusing by the ebb-tidal delta leads to strong patterns of sediment convergence and divergence along the adjacent Ocean Beach.