This study aimed at assessing the seasonal, spatial macrobenthic community structure and the impact of natural, anthropogenic effects on the benthic ecological quality of the coastal waters of Kochi, southwest coast of India. The benthic community exhibited high diversity, and species richness during the winter monsoon (WM) and spring inter-monsoon (SIM) than the southwest monsoon (SWM) season. The factors contributing to such temporal variation are the stable water column, downward flux of the surface production and recruitment process of species during the WM and SIM. The occurrence of coastal upwelling during the SWM leads to high biological production, followed by degradation of organic matter in the water column and ultimately leading to depleted oxygen levels in the coastal waters. The presence of polychaetes such as Paraprionospio pinnata, Paraprionospio sp., Magelona cincta, Heteromastus sp., Notomastus sp., Lumbrineris sp., Chaetozone sp. and Tharyx sp., in large numbers during the SWM demonstrates that they can withstand oxygen-depleted waters. High macrobenthic abundance and diversity were noticed in the mid shelf region than in the inner shelf region throughout the study period. Overall, the dominant deposit feeding type of species M. cincta, P. pinnata., Heteromastus sp. contributed similar to 83% and carnivores similar to 16% (Goniadae sp., Syllis sp., and Lumbrineris sp.), whereas only similar to 1% were filter feeders and omnivores in the study region. The low macrobenthic population in the inner shelf could be due to the high physical stress, intense fishing activities and quality of organic matter. The low BENTIX Index (mean similar to 3.5) in the inner shelf region and high in the mid shelf (mean similar to 4.2) region reveals that the inner shelf waters of Kochi are "moderate" and the mid shelf waters are "good" in terms of benthic ecological quality. [GRAPHICS] .