Abstract In this investigation, we evaluated the WAVEWATCH III (WWIII) model performances by testing the sensitivity of different input-dissipation parameterizations for the Indian seas using deep and shallow water measurements. Five input/dissipation terms of WWIII namely ST1, ST2, ST3, ST4 and ST6 have been used to simulate the significant wave parameters in the Bay of Bengal and Arabian Sea for the years 2003 and 2004. The comparisons suggest that the simulations using ST4 physics functions best; with low RMSE and PE for all the seasons. The ST2 physics was best in simulating rough weather conditions. Further, at a location off Gopalpur, the SWAN hindcast outperforms WWIII; by using ST4/ST6 physics, with low PE. The study also points out to the fact that such comparisons have limitations and hence model performance evaluation must aim to consider spectrum and source function analysis.