Water-level fluctuations are a major function of reservoirs that influence the littoral zone of the lake, and prove to be of high importance for the whole biological communities of lakes. Working on a French hydropower reservoir, we studied the influence of water-level fluctuations on intra-annual variations of littoral habitat availability and their consequences for the structure of fish assemblages inhabiting the littoral zone. As the water level decreased significantly, habitat conditions tended to be much more homogeneous. The proportion of sites with a thin substrate and low slope increased, while submerged vegetation and riparian shade disappeared. The relationship between habitat complexity and fish assemblage changed along the water-level gradient. The habitat effect on assemblage structure was strongest when the water-level conditions were high and very high, and weaker for low and very low water-level conditions. A homogenization of fish assemblages was observed when the water-level condition reached a threshold. These results suggest an effect of water-level management in structuring fish assemblages of the littoral zone of a reservoir due to a decrease of habitat complexity.