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As the global population continues to grow, sandy beaches, one of the most valuable ecosystems, have been widely impacted by human activities. Therefore, to develop policies for the conservation and management of sandy beaches, the impact of human activities on sandy beaches must be accurately assessed. We used seven benthic indices to evaluate the ecological quality of sandy beaches in Anmyeon Island, Korea. However, these seven indices were found to either over- or underestimate their ecological quality. Moreover, despite incorporating beach morphodynamics into our study, these indices did not respond to the pressure of urbanisation on beaches. Given the suboptimal performance of benthic indices in reflecting the actual state of Korean beaches, our study indicates that beaches without human interference but with the same morphodynamics must be selected as control groups to further explore the effectiveness of these indices. This is critical for advancing our conservation efforts and managing sandy beach ecosystems under increasing human influence.