Recent studies have shown that anguillid eel populations in habitats spanning the marine–freshwater ecotone can display extreme plasticity in the range of catadromy expressed by individual fishes. Carbon and nitrogen stable isotope analysis was used to differentiate between European eels (Anguilla anguilla) collected along a short (2 km) salinity gradient ranging from <1‰ to ~30‰ in Lough Ahalia, a tidal Atlantic lake system. Significant differences were recorded in mean δ13C, δ15N and C:N values from eels collected from fresh, brackish and marine-dominated basins. A discriminant analysis using these predictor variables correctly classified ca. 85% of eels to salinity zone, allowing eels to be classified as freshwater (FW), brackish (BW) or marine (MW) residents. The results of the discriminant analysis also suggested that a significant proportion of eels moved between habitats (especially between FW and BW). Comparisons of several key population parameters showed significant variation between eels resident in different salinity zones. Mean condition and estimated age was significantly lower in MW eels, whilst observed length at age (a correlate of growth) was significantly higher in MW eels, intermediate in BW and lowest in FW eels. This study has demonstrated that the ecology of eels found along a short salinity gradient can be extremely plastic and that stable isotope analysis has considerable utility in demonstrating intra-population variation in diadromous fishes.