Analysis of a series of historical bathymetric surveys has revealed large changes in morphology and sedimentation from 1856 to 1983 in San Pablo Bay, California. In 1856, the morphology of the bay was complex, with a broad main channel, a major side channel connecting to the Petaluma River, and an ebb-tidal delta crossing shallow parts of the bay. In 1983, its morphology was simpler because all channels except the main channel had filled with sediment and erosion had planed the shallows creating a uniform gently sloping surface. The timing and patterns of geomorphic change and deposition and erosion of sediment were influenced by human activities that altered sediment delivery from rivers. From 1856 to 1887, high sediment delivery (14.1 × 10⁶ m³/yr) to San Francisco Bay during the hydraulic gold-mining period in the Sierra Nevada resulted in net deposition of 259 ± 14 × 10⁶ m³ in San Pablo Bay. This rapid deposition filled channels and increased intertidal mudflat area by 60% (37.4 ± 3.4 to 60.6 ± 6.2 km²). From 1951 to 1983, 23 ± 3 × 10⁶ m³ of sediment was eroded from San Pablo Bay as sediment delivery from the Sacramento and San Joaquin Rivers decreased to 2.8 × 10⁶ m³/yr because of damming of rivers, riverbank protection, and altered land use. Intertidal mudflat area in 1983 was 31.8 ± 3.9 km², similar to that in 1856. Intertidal mudflat distribution in 1983, however, was fairly uniform whereas most of the intertidal mudflats were in the western part of San Pablo Bay in 1856. Sediment delivery, through its affect on shallow parts of the bay, was determined to be a primary control on intertidal mudflat area. San Pablo Bay has been greatly affected by human activities and will likely continue to erode in the near term in response to a diminished sediment delivery from rivers.