The trophic importance of organic matter sources to macroinvertebrate production was studied in the 4 heterogenous intertidal habitats of the Nakdong River estuary using stable isotope tracers. The isotopic signatures of the macroinvertebrate, compared with those of potential food resources, showed that food sources are diversified along their feeding strategy and habitats. Suspension feeders had a similar d¹³C to particulate organic matter in the channel while surface grazers and deposit feeders had d¹³C similar to microphytobenthos. While d¹³C range of macroinvertebrates at the P. australis-dominated habitat was broader than those at the S. triqueter-dominated and bare intertidal habitats. For quantitatively assessing the trophic base of three different habitats in the Nakdong River estuary, the relative biomass contributions of the four dietary items calculated from linear mixing model based on mass balance equations using d¹³C and d¹⁵N values were combined with macroinvertebrate carbon biomass. Despite a dramatic seasonal fluctuation in the marsh plant biomass and river discharge, the expected contribution of the marsh plant-derived and riverine organic matter did not occur. Nor the expected contribution of resuspended microphytobenthos occurred at the channel habitat. The results indicate that the food base was rather dominated by algal sources in all the different habitats.