To evaluate the modification of carbon flow in estuarine systems by a dike construction, we compared the trophic structures of the macrobenthic food webs in two contrasting estuaries, one with and one without a dike, on the western and southern coasts of Korea, by measuring the δ 13 C and δ 15 N values of subtidal macrobenthic consumers. The isotopic values of most organic matter sources were similar between the two estuaries, but there was a different pattern in the isotopic spatial variability between them. For the consumer δ 13 C values in the diked estuary, there were no significant spatial differences among sites and the isotopic niche widths were much narrower than those in the dike-free estuary. Moreover, the indices of community-wide metrics were smaller in the diked estuary than in the dike-free estuary. These results suggest a lower trophic diversity of macrobenthic consumers with their increased trophic redundancy in the diked estuary. These differences between the dike and dike-free estuaries might be explained by the decrease of benthic producers and then their lower food availabilities for consumers resulting from the presence of the dike. Our findings provide evidence that dike construction and subsequent alteration of hydrologic and circulation processes may lead to modification of the trophic structure of estuarine macrobenthic communities.