We evaluated the effects of a rehabilitation project, whose goal was to re-establish longitudinal connectivity for anadromous trout in the regulated river Emån. We used a holistic approach, by tagging and following both upstream-migrating spawners (N ¼ 348) and downstream-migrating smolts (N ¼ 80) and kelts as they passed two hydroelectric plants (HEP 2-3) with naturelike fishways.When migrating upstream, 84-88% of the spawners stopped, primarily at spawning grounds, before reaching HEP2. The proportion of stoppers was lower (56%) for fish that had been to the fishways in previous years, indicating that the recolonization rate is likely to increase over time. Of the spawners that approached the fishway at HEP2, 77% rapidly located the fishway situated next to the tail-race, resulting in an attraction efficiency of 81% and a passage efficiency of 95%. The time required to locate the fishway inside the former channel at HEP3 was substantial, but the attraction efficiency (89%) and passage efficiency (97%) were nevertheless high.The kelts swam downstream mainly in spring, using spill gates and the fishways, to swim past HEP2 and 3 and continue downstream to the Baltic Sea. Iteroparity was confirmed by the fact that 20% of the spawners were tagged in previous years. Smolt loss was about 30% for both HEPs, with a higher turbine-induced loss 30% for fish passing through Francis runners than a Kaplan runner. Fifteen per cent of the tagged smolt reached the sea and none of these fish had swum through the Francis runners.It will probably take many years before longitudinal connectivity is fully re-established in the river Emån, due to substantial losses of both upstream-migrating spawners (35% loss) and downstream-migrating smolts (50%) and kelts. In addition, smolt production in areas upstream of HEP3 is far below carrying capacity. Thus, additional measures that not only facilitate movement of upstream spawners, but also reduce mortality and injuries of downstream migrants are urgently needed to create a self-sustaining fish population.