Lake Bourget (France) provides drinking water and is a place for professional and recreational fishing. Since the mid 1990s, the lake has been exhibiting blooms of the filamentous cyanobacterium Planktothrix rubescens. This species is able to produce microcystin-LR and RR, toxins that contaminate different fish tissues and, if concentrated in the liver, can induce fish mortality. However, data on fish exposure to these toxins in a natural environment are scare and comparisons of spatial distribution between P. rubescens and exploited fish are needed to determine whether these fish avoid or converge in zones affected by the cyanobacteria. From June to November 2009, diurnal data on P. rubescens and whitefish (Coregonus lavaretus) spatial distributions have been monitored by hydroacoustic and BBE probe sampling. For all water samples, intracellular microcystin concentration of P. rubescens was quantified by HPLC/PDA. Furthermore, an arbitrary sample of eight whitefish captured at the moment of highest P. rubescens concentration in the lake were analyzed to investigate both the presence of this cyanobacterium in the gastrointestinal tract by optical microscopy and the possible bioaccumulation of the microcystin in their tissues by liquid chromatography–tandem mass spectrometry. Results show that P. rubescens abundance was at a maximum between the end of July and the beginning of September. During this period, P. rubescens abundance was vertically stratified with a maximum around 14–22 m, depending on the sampling station. The horizontal distributions of P. rubescens were heterogeneous at the scale of the lake. Results indicate that the presence of P. rubescens, for the observed cyanobacterial abundance, does not exert a significant pressure on the distribution pattern of the whitefish. Whitefish were present in the same areas as P. rubescens maxima during daytime, and they do not avoid or seek out the zone of high P. rubescens abundance. Filaments of P. rubescens have been observed in intestinal tracts of whitefish and the presence of microcystin-LR has been detected in their intestine and liver. Consequently, because of a direct contact between these organisms, toxins can be incorporated into whitefish by ingestion of P. rubescens filaments, leading to potential adverse effects on the health of this species.