The brackish water clam, Corbicula japonica, acts as an ecosystem engineer in estuaries. To identify its resource-use patterns in the low-turbidity temperate Seomjin River estuary of Korea, we analyzed stable isotope and fatty acid (FA) biomarkers to differentiate allochthonous and autochthonous dietary sources, and examined the effects of clam size, salinity gradient, and season. The δ¹³C and δ¹⁵N values were consistent across the three factors. The δ¹³C values of the clams were similar to those of both riverine- and estuarine-suspended particulate organic matter (R- and E-SPOM), while their δ¹⁵N values were 2–4‰ higher, indicating an equal contribution of both sources to the clam diet. Biogeochemical proxies and FA compositions of SPOM indicate that estuarine phytoplankton significantly contribute to the E-SPOM pool. Moreover, the similarity in FA profiles between Corbicula and E-SPOM indicates that phytoplankton-derived organic matter is the primary source of nutrition for the clam, with minimal impact from growth, salinity gradient, or seasonal changes. Our study suggests that in low-turbidity estuaries with high phytoplankton production, allochthonous organic matter makes a negligible contribution to clam nutrition, compared to high-turbidity estuaries. This finding could provide insights into the variations in the trophic structure of estuarine food webs across diverse regions.

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