The highly urbanized estuary of San Francisco Bay is an excellent example of a location susceptible to flooding from both coastal and fluvial influences. As part of developing a forecast model that integrates fluvial and oceanic drivers, a case study of the Napa River and its interactions with the San Francisco Bay was performed. For this application we utilize Delft3D-FM, a hydrodynamic model that computes conservation of mass and momentum on a flexible mesh grid, to calculate water levels that account for tidal forcing, storm surge generated by wind and pressure fields, and river flows. We simulated storms with realistic atmospheric pressure, river discharge, and tidal forcing to represent a realistic joint fluvial and coastal storm event. Storm conditions were applied to both a realistic field-scale Napa river drainage as well as an idealized geometry. With these scenarios, we determine how the extent, level, and duration of flooding is dependent on these atmospheric and hydrologic parameters. Unsurprisingly, the model indicates that maximal water levels will occur in a tidal river when high tides, storm surge, and large fluvial discharge events are coincident. Model results also show that large tidal amplitudes diminish storm surge propagation upstream and that phasing between peak fluvial discharges and high tide is important for predicting when and where the highest water levels will occur. The interactions between tides, river discharge, and storm surge are not simple, indicating the need for more integrated flood forecasting models in the future.