Habitat fragmentation is a critical anthropogenic stressor leading to the decline of biodiversity, as it prevents species reaching essential habitat to complete their life cycle. A flagship species affected by habitat fragmentation, is the European eel (Anguilla anguilla L.). The European eel is a catadromous fish species, meaning it spawns in the marine environment, but grows in freshwater systems. Hency, they need to migrate between the two realms, requiring habitat connectivity. Due to hydrological management, artificial structures have been created acting as migration barriers for the eels: tidal sluices, water pumping stations, shipping lock complexes and weirs are some examples. In this PhD thesis, we tagged and tracked seaward migrating eels by means of acoustic telemetry in three different stystem: an estuary, a polder system and a shipping canal. The estuary served as a case without migration barriers, illustrating the eels were not obstructed nor delayed. To migrate in a bioenergetic efficient way towards the sea, the eels applied selective tidal stream transport. The polder and shipping canal are obstructed by a water pumping station and shipping locks respectively. In this dissertation, we illustrated that these migration barriers substantially hampered silver eel migration via delays, disorientation and exploratory behaviour. Therefore, adequate management measures such as fish friendly screws in the pumping stations, fish passages or gravitational flow stimulation during specific migration windows need to be taken to aid recovery of the European eel population. Such management demands a constructive cooperation between ecologists and engineers. Not only the European eel, but other diadromous and potamodromous fish species will benefit from this as well.