To understand the sedimentary environment of Scirpus planiculmis habitat (Myeongji and Eulsuk tidal flats) in the Nakdong Estuary, this study analyzed the statistical parameters (sorting, skewness, and kurtosis) of grain size data and the major (Al, Fe, Mn, Mg, Ca, Na, K, Ti, and P), minor (Li, Sc, V, Cr, Co, Ni, Cu, Zn, Sr, Zr, Cs, Pb, Th, and U), and rare earth elements (REEs) in sediment cores. For Myeongji, the sediment structure of the upper part of the cores was poorly sorted, more finely skewed, and more leptokurtic due to construction of the West gate. By contrast, the Eulsuk cores all differed due to the contrasting floodgate operation patterns of the West and East gates. The linear discriminate function (LDF) results corresponded to the statistical parameters for grain size. At the Eulsuk tidal flat (sites ES05 and ES11), elemental distributions were representative of Al-, Fe- and Ca-associated profiles, in which the elements are largely controlled by the accumulation of their host minerals (such as Na- and K-aluminosilicate and ferromagnesium silicate) and heavy detrital minerals at the sites. Detrital minerals including the aluminosilicates are major factors in the elemental compositions at ES05, diluting the REE contents. However, clay minerals and Fe-oxyhydroxides, as well as REE-enriched heavy minerals, appeared to be controlling factors of the elemental composition at ES11. Therefore, the mineral fractionation process is important in determining the elemental composition during sedimentation, which reflects the depositional condition of riverine-saline water mixing at both sites.