The global population of European eel (Anguilla anguilla) is rapidly declining, and migration barriers in rivers are believed to be one of several key causes. While progress has been made in the development of bypass solutions, they are often constructed based on a limited knowledge of swimming behaviour. A bypass close to the stream bed is often recommended at fish passage facilities to accommodate downstream eel migration. The results of this recommendation are poorly studied, and the few studies that exist show varying bypass efficiencies. The current study used acoustic telemetry with depth sensors to explore the three-dimensional migratory behaviour of downstream-migrating silver eels. The eels were tracked as they approached a hydropower plant with a state-of-the-art angled bar rack and full-depth bypass. Downstream and upstream swimming differed in preferred vertical and lateral positions. During periods of local downstream movement, the density of observations was largest in the upper middle section, away from the river boundaries and in higher velocities. Conversely, when moving upstream, eels tended to avoid the upper layers of the middle part of the river, swimming closer to the riverbed and using the bank areas to a greater extent. Downstream-moving fish swam higher in the water column during night and in turbid conditions (high discharge). When approaching the impassable bar rack and the full-depth bypass, the eels searched most intensely but not exclusively along the bottom third of the rack, often exploring at new depths after changing direction. The impediment passage efficiency was 100% when both bypass solutions were considered. The study provides knowledge of the swimming behaviour of silver eels, which is relevant for the design of bypass solutions for eels at migration barriers.