Studies of core sediments and seismic reflection profiles elucidate the structure and depositional history of Bolinas Lagoon, Calif., which covers 4.4 km 2 and lies in the San Andreas fault zone at the southeast corner of the Point Reyes Peninsula 20 km northwest of San Francisco. The 1906 trace of the San Andreas fault crosses the west side of the lagoon and was determined from (1) tectonically caused salt-marsh destruction indicated by comparison of 1854 and 1929 U.S. Coast and Geodetic Survey (U.S.C. & G.S.) topographic surveys, (2) formation of a tidal channel along the border of destroyed salt marshes, and (3) azimuths of the trend of the fault measured in 1907. Subsidence in the lagoon of 30 cm occurred east of the San Andreas fault in 1906. Near the east shore, seismic-reflection profiling indicates the existence of a graben fault that may connect to a graben fault on the Golden Gate Platform. Comparison of radiocarbon dates on shells and plant debris from boreholes drilled on Stinson Beach spit with a relative sea-level curve constructed for southern San Francisco Bay indicates 5.8 to more than 17.9 m of tectonic subsidence of sediments now located 33 m below mean sea level. Cored sediments indicate a marine transgression dated at 7770?65 yrs B.P. overlying freshwater organic-rich lake deposits. Fossil pollen including 2 to 8 percent Picea (spruce) indicate a late Pleistocene (?)-Early Holocene climate, cooler, wetter, and foggier than at present. Above the transgression are discontinuous and interfingering sequences of transgressive-regressive marine, estuarine, and barrier sediments that reflect rapid lateral and vertical shifts of successive depositional environments. Fossil megafauna indicate (1) accumulation in a protected, shallow-water estuary or bay, and (2) that the lagoon was probably continuously shallow and never a deep-water embayment. Analysis of grain-size parameters, pollen frequencies, and organic remains from a core near the north end of the lagoon indicates (1) that mid-nineteenth-century redwood logging correlates with rates of sediment accumulation of l.3 to 1.9 cm/yr that are three to 6 times higher than post-1906 rates of 0.3 to 0.4 cm/yr, (2) accumulation of up to 115 cm of sediment since 1849, and (3) an anomalously coarse-grained sediment that may correlate with the 1906 earthquake.