Coupled process based model incorporating the atmosphere-wave-ocean interactions has been developed to investigate wave and storm surge in the region of extremely shallow waters. An additional shear stress, due to wave energy dissipation using the roller concept within the surface boundary layer, is introduced in this system to consider the processes of energy transfer from wind to current through wave process. Hindcast simulation of storm surge for 2005 Hurricane Katrina in this study has demonstrated the importance of energy transfer path via whitecap dissipation of wind waves in the generation mechanism of mean current in the shallow waters. It is also shown that the atmosphere-wave-ocean coupling model system using designed coupler adopted in this study is a feasible system for understanding wave and storm surge dynamics.