Mercury (Hg) is a global pollutant, which specially affects aquatic ecosystems, both marine and freshwater. Top-predators depending on these environments, such as seabirds, are regarded as suitable bioindicators of Hg pollution. In the Ebro Delta (NE Iberian Peninsula), legacy Hg pollution from a chlor-alkali industry operating in Flix and located ca. 100 km upstream of the Ebro River mouth has been impacting the delta environment and the neighboring coastal area. Furthermore, natural occurring levels of Hg in the Mediterranean Sea are known to be high compared to other marine areas. In this work we used a Hg stable isotopes approach in feathers to disentangle the Hg sources and processes leading to different Hg concentrations in three Laridae species breeding in sympatry in the area (Audouin’s gull Ichtyaethus audouinii, black-headed gull Chroicocephalus ridibundus, common tern Sterna hirundo; N = 10 individuals for each species). These species have distinct trophic ecologies and make a different use of marine resources (mesopelagic and epipelagic fishes) and rice paddies prey. Moreover, for Audouin’s gull in which in the Ebro Delta colony temporal differences in Hg levels were documented previously, we investigated the change in the contribution of different Hg sources using the same approach. Hg stable isotopes differentiated the three different species according to their trophic ecologies. Furthermore, for Audouin’s gull we observed temporal variations in Hg isotopic signatures possibly owing to anthropogenic-derived pollution in the Ebro Delta. To the best of our knowledge this is the first time Hg stable isotopes have been reported in seabirds from the NW Mediterranean.