Modeling geomorphic evolution in estuaries is necessary to model the fate of legacy contaminants in the bed sediment and the effect of climate change, watershed alterations, sea level rise, construction projects, and restoration efforts. Coupled hydrodynamic and sediment transport models used for this purpose typically are calibrated to water level, currents, and/or suspended-sediment concentrations. However, small errors in these tidal-timescale models can accumulate to cause major errors in geomorphic evolution, which may not be obvious. Here we present an intermediate step towards simulating decadal-timescale geomorphic change: calibration to estimated sediment fluxes (mass/time) at two cross-sections within an estuary. Accurate representation of sediment fluxes gives confidence in representation of sediment supply to and from the estuary during those periods. Several years of sediment flux data are available for the landward and seaward boundaries of Suisun Bay, California, the landward-most embayment of San Francisco Bay. Sediment flux observations suggest that episodic freshwater flows export sediment from Suisun Bay, while gravitational circulation during the dry season imports sediment from seaward sources. The Regional Oceanic Modeling System (ROMS), a three-dimensional coupled hydrodynamic/sediment transport model, was adapted for Suisun Bay, for the purposes of hindcasting 19th and 20th century bathymetric change, and simulating geomorphic response to sea level rise and climatic variability in the 21st century. The sediment transport parameters were calibrated using the sediment flux data from 1997 (a relatively wet year) and 2004 (a relatively dry year). The remaining years of data (1998, 2002, 2003) were used for validation. The model represents the inter-annual and annual sediment flux variability, while net sediment import/export is accurately modeled for three of the five years. The use of sediment flux data for calibrating an estuarine geomorphic model guarantees that modeled geomorphic evolution will not exceed the actual supply of sediment from the watershed and seaward sources during the calibration period. Decadal trends in sediment supply (and therefore fluxes) can accumulate to alter decadal geomorphic change. Therefore, simulations of future geomorphic evolution are bolstered by this intermediate calibration step.