Coupled ocean-atmospheric phenomenon such as tropical cyclones (TC's) is governed by geophysical fluid dynamics. TC associated strong wind stress transfer momentum energy to the ocean surface that acts as the prime mechanism in modulating the sea surface and in generating the storm surge. A primitive equation, Princeton ocean model (POM) with free surface, sigma (terrain-following) coordinates and realistic bottom topography is configured in Bay of Bengal (BoB) to simulate the storm surge/sea surface height (SSH) and surface currents during a super cyclone TC05B 1999. TC wind fields are developed by adopting a suitable formulation based on partial conservation of angular momentum. Modeled TC wind fields are superimposed with QuikSCAT Satellite/National Centre for Environmental Prediction (QSCAT/NCEP) blended ocean surface winds to drive the three-dimensional ocean model. Model simulated storm surge and SSH are compared with limited available surge estimates/observations and multi-satellite observed AVISO (Archive, Validation and Interpolation of Satellite Oceanography) SSH, respectively to evaluate its performance.