Accurate and timely flood forecasts are critical for making emergency-response decisions regarding public safety, infrastructure operations, and resource allocation. One of the main challenges for coastal flood forecasting systems is a lack of reliable forecast data of large-scale oceanic and watershed processes and the combined effects of multiple hazards, such as compound flooding at river mouths. Offshore water level anomalies, known as remote Non-Tidal Residuals (NTRs), are caused by processes such as downwelling, offshore wind setup, and also driven by ocean-basin salinity and temperature changes, common along the west coast during El Niño events. Similarly, fluvial discharges can contribute to extreme water levels in the coastal area, while they are dominated by large-scale watershed hydraulics. However, with the recent emergence of reliable large-scale forecast systems, coastal models now import the essential input data to forecast extreme water levels in the nearshore. Accordingly, we have developed Hydro-CoSMoS, a new coastal forecast model based on the USGS Coastal Storm Modeling System (CoSMoS) powered by the Delft3D San Francisco Bay and Delta community model. In this work, we studied the role of fluvial discharges and remote NTRs on extreme water levels during a February 2019 storm by using Hydro-CoSMoS in hindcast mode. We simulated the storm with and without real-time fluvial discharge data to study their effect on coastal water levels and flooding extent, and highlight the importance of watershed forecast systems such as NOAA’s National Water Model (NWM). We also studied the effect of remote NTRs on coastal water levels in San Francisco Bay during the 2019 February storm by utilizing the data from a global ocean model (HYCOM). Our results showed that accurate forecasts of remote NTRs and fluvial discharges can play a significant role in predicting extreme water levels in San Francisco Bay. This pilot application in San Francisco Bay can serve as a basis for integrated coastal flood modeling systems in complex coastal settings worldwide.