The objectives of the present studywere to evaluate the ecological status of tropical coastalwaters using the temperate benthic indices and examine the effect of seasonal variability on the performance of benthic indices. Macrobenthic sampleswere collected fromnorthwest to southeast coast of India during 2003–2012 andwe tested different univariate indices, ecological strategies, indicator species and multimetric indices. AMBI and multimetric indices performed satisfactorily in evaluating the ecological status. Seasonal variability on the biotic indices was observed during the southwest monsoon and fall intermonsoon period due to recruitment. Therefore, we recommended the non-monsoon period (January–May) as a suitable time of the year to use the indices for effective assessment of the Indian coastal waters. Results show that, the temperate benthic indices are efficient in assessing the tropical environmental status. However, complementary use of different indices is suggested for accurate assessment of the environmental status.