Anthropogenic activities in watersheds can have profound effects on sediment transport through river systems to estuaries. Disturbance in a watershed combined with alterations to the hydro-climatologic regime may result in changes to the sediment flux, and exacerbate the impacts of extreme events (such as large-magnitude floods) on sediment transport. In the San Francisco Estuary, suspended sediment has been declining over the past 30 years as a result of declining sediment supply, contributing to dramatic changes in the ecology and geomorphology of the estuary. However, the decline has not been gradual. Recent observations of an abrupt decrease in suspended sediments in the San Francisco Bay have been explained by a model that suggests that the step change has occurred due to exceedance of a sediment regulation threshold that triggered the change from a sediment transport regime to a supply-limited system. We investigated structural changes in the historical record of total suspended solids (TSS) concentration measured in the upper estuary to verify the model predictions. TSS in the upper estuary exhibited an abrupt step decrease in 1983 corresponding to the record-high winter and summer flows from the 1982 to 1983 El Niño event. After this step change, TSS concentrations had a significant declining trend despite subsequent near-record high flows. The abrupt change in TSS followed by the declining trend provides evidence for the hypothesis of sediment supply limitation in the San Francisco Estuary.