The population of European silver eel Anguilla anguilla has declined tremendously in the last decades. The cause of this decline is unknown, and it is necessary to investigate the migratory behaviour and survival rates of silver eels during the reproductive migration in order to understand if the decline is related to factors acting during that migration. We estimated survival and progression rates of European silver eel migrating in the lower part of the River Gudenaa and during the first phase of the marine migration in the Randers Fjord in Denmark. Fifty migrating silver eel (total body length: 56 to 84 cm) were captured, and each was equipped with an acoustic transmitter. Their migration was subsequently monitored using an array of automatic listening stations, and progression rate and mortality in the river, inner part of the fjord and outer part of the fjord were estimated. Survival was high in fresh water. However, 60% of eels were lost in the inner and outer fjord, supporting the hypothesis that mortality is large in the early phase of the marine migration and that fishing may be a major cause of mortality of silver eels. There was no indication that the slowest-migrating individuals were more prone to fishing mortality than the faster-migrating individuals. Progression rate increased as the eels proceeded downriver and out of the fjord. The migration was predominantly nocturnal, both in the river and fjord. Based on the available evidence, a considerable increase in eel survival in the river–fjord system will be needed in order to fulfil the goals in the European Union recovery plan for eels.