The vertical and horizontal distribution of the cyanobacterium, Planktothrix rubescens, was studied in a deep alpine lake (Lac du Bourget) in a 2-year monitoring program with 11 sampling points, and a 24-h survey at one sampling station. This species is known to proliferate in the metalimnic layer of numerous deep mesotrophic lakes in temperate areas, and also to produce hepatotoxins. When looking at the distribution of P. rubescens at the scale of the entire lake, we found large variations (up to 10 m) in the depth of the biomass peak in the water column. These variations were closely correlated to isotherm displacements. We also found significant variations in the distribution of the cyanobacterial biomass in the northern and southern parts of the lake. We used a physical modeling approach to demonstrate that two internal wave modes can explain these variations. Internal waves are generated by wind events, but can still be detected several days after the end of these events. Finally, our 24-h survey at one sampling point demonstrated that the V1H1 sinusoidal motion could evolve into nonlinear fronts. All these findings show that internal waves have a major impact on the distribution of P. rubescens proliferating in the metalimnic layer of a deep lake, and that this process could influence the growth of this species by a direct impact on light availability.