Estuaries are one of the most productive regions in ecosystems and serve as important nursery and recruitment habitats for various living resources. However, information on the trophic dynamics of estuarine copepods along the salinity gradient is not well known. Here, we investigated resource partitioning among three copepods, Pseudodiaptomus japonicus, Sinocalanus tenellus, and Tortanus dextrilobatus in the Seomjin River estuary of the Korea using stable carbon and nitrogen isotope analyses. Among the three copepods, S. tenellus showed the lowest δ13C values, while the highest δ13C values were observed in T. dextrilobatus. Stable Isotope Analysis in R (SIAR) showed that S. tenellus fed mainly on terrestrial particulate organic matter (POM), while the contribution of marine POM was relatively high in the diet of T. dextilobatus. In contrast, P. japonicus showed relatively high trophic flexibility between terrestrial and marine POM. Thus, the Stable Isotope Bayesian Ellipses in R (SIBER) showed no dietary niche overlap among the three copepods. Therefore, we suggest that the coexistence of S. tenellus, P. japonicus, and T. dextrilobatus in the Seomjin River estuary can be closely associated with species-specific differences in resource utilization along the salinity gradient.