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To determine distributions, bioaccumulation, and trophic transfer of freshwater cyanobacterial toxins such as microcystins (MCs), surface water, suspended solids, sediments, and coastal organisms were collected from seven stations in inner and outer regions of the estuary dam in the Geum River Estuary in June and July 2017. Concentrations of MC variants (MC-LR, -RR, and -YR) in the multimedia samples were analyzed using a HPLC-MS/MS. Trophic position (TP) of organisms (fish, bivalve, gastropod, decapod, and polychaete) was determined by nitrogen stable isotope analyses of both bulk tissues and amino acids. From July to August 2017, great concentrations of MCs were detected in discharged freshwater ranging from 0.4 to 75 μg L⁻¹. Considerable amounts of MCs are delivered to the Geum River Estuary in summer season. MCs spread far away as dissolved phases (18.7–49.5 ng L⁻¹) in July when …