A 3-dimensional Princeton Ocean Model has been configured for the east coast of India, which is applied to study the transformation of the upper ocean's response in the near-coastal waters to the 1999 Orissa super cyclone in the Bay of Bengal at the time of landfall. It is well known that the sea surface temperature (SST) cooling is more towards the right of the storm track, because of the dominant wind stress forcing there. Consequently, the model simulated SSTs showed more cooling to the right of the storm track. However, it is found to be true only in the open ocean. The coastal dynamics transformed the scenario as the cyclone translated over the coastal waters owing to the impedance of the coast-line to the circulation and shifted the region of maximum surface cooling to the left of the cyclone track. The satellite imageries during the period also endorsed the model simulations.