The aim of this study was to investigate differences in d 13 C and d 15 N of pond smelt (Hypomesus nipponensis) collected from three brackish lagoons, which have different characteristics, the principal one being the presence or absence of a weir located near the mouth of the outlet channel. The presence or absence of a weir is reflected in a difference in salinity among the study lakes. We found a general pattern of lower pond smelt d 13 C values in Lake Mae with lower salinity and higher pond smelt d 13 C values in Lake Hwajinpo and Lake Youngrang (lagoons with higher salinity). Pond smelt d 13 C values showed little variation among the three lagoons related to pond smelt length, but likely reflected the availability of freshwater prey in Lake Mae. Among the lagoons, we found that pond smelt d 15 N values were lower in Lake Hwajinpo compared with pond smelt d 15 N values in Lake Youngrang and Lake Mae. This pattern likely shows a difference in anthropogenic nitrogen (N) loading among the lagoons. The results of this study emphasize the utility of stable isotope measurements to better understand how structural characteristics of aquatic ecosystems (presence or absence of a weir) and anthropogenic disturbances can affect stable isotope patterns in aquatic food webs. This stable isotope approach may be a general technique for evaluating fish habitat and restoration or management of coastal lagoon ecosystems.