Knowing the way individuals use their environment is crucial to undertake relevant measures of restoration or mitigation of the ecosystems they inhabit. In this study we evaluated the habitat preferences of three piscivorous species, pikeperch (Sander lucioperca), pike (Esox lucius) and perch (Perca fluviatilis), in a French reservoir impacted by water level fluctuations. Our objective was then to assess the impact of hydrological variations on these habitat preferences. Sixty adults have been monitored by acoustic telemetry for two years. By classifying each fish position either into the littoral zone or into the central zone, the intensity of use of each one was assessed. In the littoral zone, the habitat types have been described by substrate size, vegetation type, tree stumps and undercut banks. Linking the fish positions to the habitat types allowed to evaluate the habitat preferences. Our results show that seasonal variations in the intensity of use of the littoral and central zones are significant for the three species whereas these variations in littoral habitat preferences are less obvious. They highlight species-specific patterns but high individual variability. Water level fluctuations only slightly modify these main seasonal patterns by changing the availability of the different habitats.