This paper presents a method of integrating hydrodynamic modeling with frequency analysis to predict a 100-year storm surge in the coastal waters of Pensacola Bay, Florida. The ADCIRC hydrodynamic model was applied to Pensacola Bay, and was calibrated by using observations of water levels from the storm surge of Hurricane Ivan in 2004. The calibrated hydrodynamic model was used to predict extreme flood areas in Pensacola Bay, and was based on the frequency analysis of annual maximum water levels at the NOAA station in the Bay. The water levels of a 100-year return period at the NOAA station were obtained from frequency analysis, and further used to derive a synthetic storm-surge hydrograph at the ocean boundary. Under the gravity forcing as specified in 100-year boundary storm surge hydrograph, hydrodynamic modeling was conducted to predict spatial distributions of maximum water levels in the bay. The model prediction of a water level of 3.2 m at the NOAA station matches well with that from the frequency analysis of 100-year water elevation, and indicate that maximum water levels are affected by the wind.