Macrobenthic communities are useful biological indicators for monitoring the health status of marine environments. In this context, biological indices have been widely developed based on macrobenthic communities in order to distinguish the ecological status of marine environments. In this study, results from several indices such as Shannon–Weiner, AZTI Marine Biotic Index, Multimetric AZTI Marine Biotic Index, and BENTIX were compared and evaluated. The effects of environmental factors on the benthic communities were also studied. Results from these indices revealed significant differences in ecological status between sampling stations, which were probably due to the different structures of benthic communities and their state successions. The results consistently emphasized the anthropogenic effects and natural variability caused by these variations in spatial scales.