This study aimed to describe the effect of cormorant predation on newly established Atlantic salmon, Salmo salar, population in three nursery streams in the upper Elbe River basin (Czech Republic). Salmon have been annually stocked into the nursery streams since 1998 as part of a salmon reintroduction programme. Salmon parr density in nursery streams was 3–81 fish per 100 m². Only thirteen adult salmon were observed in the study area during two years of research. Altogether 912 cormorant pellets were collected, 5482 diagnostic bones were analysed, and 3915 fish were identified in the diet. Cormorant diet was composed of 24 fish species from six families but no salmon were consumed. The salmon stocking programme produces a reasonable amount of smolts but return rates of adults are very low. The cause of low return rates is not cormorant predation on nursery streams but, most likely, a low survival rate on the passage downstream. We suggest that more studies should focus on monitoring of survival and return rates of salmon in the upper River Elbe to ensure that, in the future, the salmon reintroduction programme will be really successful.