Hydraulic structures such as navigation locks, pumping stations and hydropower plants play an important role in navigation, water management and sustainable energy production. However, these structures may severely impact the aquatic ecosystem and freshwater fish in particular. In Belgium, the Albert Canal connecting the river Meuse to the river Scheldt, is an important migration route for European eel (Anguilla anguilla, critically endangered) and Atlantic salmon (Salmo salar, vulnerable). Both species have a downstream migrating phase in their lifecycle (respectively silver eels and salmon smolts), during which they are hampered by hydraulic structures. In the coming years, Archimedes screws are to be installed at the navigation lock complexes present in the Flemish part of the canal, which can function both as pumping stations and hydropower generators. A first installation is already present at the navigation lock complex of Kwaadmechelen. Before fish mitigation measures can be implemented, it is important to gain understanding on how the downstream migrating fish are affected by hydrodynamics around the complex. In this paper, we focus on the challenges in investigating fish behaviour, related to the acoustic telemetry used to determine fish positions, as well as on the complexity of a hydrodynamic CFD model for the studied site. Additionally, we present some preliminary results. In the next phase of the research, observed fine-scale behaviour of the fish in front of the navigation lock complex will be compared with predicted flow patterns by means of a CFD model