River flow and sediment transport in estuaries influence morphological development over decadal and century time scales, but hydrological and sedimentological records are typically too short to adequately characterize long-term trends. In this study, we recover archival records and apply a rating curve approach to develop the first instrumental estimates of daily delta inflow and sediment loads to San Francisco Bay (1849 – 1929). The total sediment load is constrained using sedimentation/erosion estimated from bathymetric survey data to produce continuous daily sediment transport estimates from 1849 to 1955, the time period prior to sediment load measurements. We estimate that ~55% (45 – 75%) of the ~1500±400 million tons (Mt) of sediment delivered to the estuary between 1849 and 2011 was the result of anthropogenic alteration in the watershed that increased sediment supply. Also, the seasonal timing of sediment flux events has shifted because significant spring-melt floods have decreased, causing estimated springtime transport (April 1st to June 30th) to decrease from ~25% to ~15% of the annual total. By contrast, wintertime sediment loads (December 1st to March 31st) have increased from ~70% to ~80%. A ~35% reduction of annual flow since the 19th century along with decreased sediment supply has resulted in a ~50% reduction in annual sediment delivery. The methods developed in this study can be applied to other systems for which unanalyzed historic data exist.