With the increasing economic and social activities along with the increasing frequency as well as the intensity of hurricanes, the coastal regions are at greater risk of flooding and storm surges than before. A three-dimensional hydrodynamic model using Environmental Fluid Dynamics Code Plus (EFDC+) was developed to study the impacts of different intensities of hurricanes without and with the implementation of Natural and Nature-Based Features (NNBFs) along Mobile Bay, AL. The external driving forces for the model include the inflows from two major rivers (Mobile River and Tensaw River), atmospheric winds, tropical cyclones, and the harmonics tides or water level at the open boundaries, on the south where flow exchange takes place. Hurricane Ivan (2004) and Hurricane Sally (2020) were used for model calibration and verification. The simulated water surface elevations (WSEL) were compared against the observed data at different monitoring stations within Mobile Bay with good agreement. The calibrated EFDC+ model was used to study the response of the bay under two different Hurricane scenarios, one was based on the storm events with seven different return periods, provided by Hazus application, and another was based on hypothetical worst-case approach with three different hurricane track directions. The low lying northern coastal region of Mobile County was mostly flooded by all major hurricanes (Categories 3 and above). The area near the Mobile Regional Airport was the most impacted region in different scenario runs and selected to test different scenarios of NNBFs, vegetations with three different plant densities, artificial reefs, artificial sand dunes, and artificial sand dunes with vegetation. Four different parameters: water depth, velocity, flow, and bed shear, were compared before and after the implementation of NNBFs. The installation of artificial sand dunes provided greater reduction in water depths, velocities, flows, and bed shear as compared to other tested NNBFs. The results were even better for the combined use of sand dunes along with the vegetations.