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During economic growth, anthropogenic activities have exerted detrimental impacts on the tidal flat ecosystems in South Korea. Although scholars have conducted extensive research on the ecological quality of tidal flats in South Korea, most have primarily focused on benthic indices. Hence, we utilised two heavy metal indices and five benthic indices to assess the ecological quality in the tidal flats comprehensively. In our study, although heavy metals and total organic carbon concentrations were low in Garolim Bay, the final ecological quality at most stations was unacceptable (63%). The Benthic Opportunistic Polychaetes Amphipods Index (BOPA) demonstrated commendable outcomes in correlation and kappa analyses. However, the BOPA still had some limits. We believe that using multiple indices to assess the ecological quality in the tidal flats of Garolim Bay is more robust than using a single index.