This study deals with the macrobenthic assemblages and the biotic environmental quality of Kochi backwaters (KBW), India. Due to the heavy river discharge, extensive limnetic and turbid conditions prevailed in the KBW during the southwest monsoon (June to September). This exerted a profound adverse effect on the abundance, richness, and diversity of macrobenthic assemblages. Overall, mesohaline conditions with a clayey sand bottom substratum favored the high macrofaunal abundance during the southwest and northeast monsoon seasons. But mesohaline condition and sandy silt bottom were found to support high macrofaunal abundance in the KBW during the pre-monsoon season. Polychaete dominated the macrobenthic community, regardless of seasons. Capitella capitata, Heteromastus similis, Paraheteromastus sp., Prionospio cirrobranchiata, Minuspio cirrifera, Pagurapseudopsis kochindica, P. gymnophobia, Ctenapseudes indiana, C.chilkensis, Tanais sp., Villorita cyprinoides, Grandidierella sp., Ampelisca sp., and Littorina sp. were the dominant ones observed during the study. The sediment organic carbon, in general, showed a positive correlation with polychaete abundance during all three seasons. The ecological status of KBW during all three seasons was assessed as per BO2A index, which ranged from 0.05 to 0.18, suggesting a healthy to a moderately polluted bottom environmental condition.