The foraging of Great Cormorants Phalacrocorax carbo in Alpine rivers is a relatively recent phenomenon. Wintering populations in Slovenia increased in the 1980s. In the 1990s, the increase affected the upper sections of rivers where the habitats of Grayling Thymallus thymallus and trout Salmo and Oncorhynchus spp. are located. The upper section of the Soča River system is known as one of the biogeographic hotspots for (sub)alpine rivers, where several endemic or rare fish species are found. The aim of this study is to evaluate the diet of the Cormorants in this area and to compare it to some other threats to the fish fauna of the river. A total of 75 Cormorant stomachs were examined. Of these, 68 (90.7%) contained fish or recognisable fish remains. The birds' diet consisted of eight species of fish: Marble Trout, Rainbow Trout, Common Nase, Vairone, Common Chub, Italian Chub, Italian Barbel and Bullhead. The increase in numbers and the diet of Cormorants in the river basin of Soča is discussed in the context of the increase of other threats to this ecosystem, such as fish stocking, gravel extraction and tourism, especially angling and water sports. A more comprehensive environmental assessment of all these factors is needed, as their increase runs parallel with the arrival of the Cormorants in the upper section of the river. There is therefore reason to believe that Cormorants are only a small part of a larger problem in the conservation of the river ecosystem.