Recent modeling has demonstrated that sediment supply is one of the primary environmental variables that will determine the sustainability of San Francisco Estuary tidal marshes over the next century as sea level rises. Therefore, understanding the environmental controls on sediment flux within the San Francisco Estuary is crucial for optimal planning and management of tidal marsh restoration. Herein, we present suspended-sediment flux estimates from water year (WY) 2009–2016 from the San Francisco Estuary to investigate the environmental controls and impact of the record 2013–2016 California drought. During the recent drought, sediment flux into Lower South Bay, the southernmost subembayment of the San Francisco Estuary, increased by 345% from 114 kt/year from WY 2009 to 2011 to 508 kt/year from WY 2014 to 2016, while local tributary sediment flux declined from 209 to 51 kt/year. Total annual sediment flux from WY 2009 to 2011 and 2014 to 2016 can be predicted by total annual freshwater inflow from the Sacramento-San Joaquin Delta (R² = 0.83, p < 0.01), the primary source of freshwater input into the San Francisco Estuary. The volume of freshwater inflow from the Sacramento-San Joaquin Delta is hypothesized to affect shoal-to-channel density gradients that affect sediment flux from broad, typically more saline and turbid shoals, to the main tidal-channel seaward of Lower South Bay. During the drought, freshwater inflow from the Sacramento-San Joaquin Delta decreased, and replacement of typically more saline shoal water was reduced. As a result, landward-increasing cross-channel density gradients enhanced shoal-to-channel advective flux that increased sediment available for tidal dispersion and drove an increase in net-landward sediment flux into Lower South Bay.