Polycyclic aromatic hydrocarbons (PAHs) were detected in different types of PAH-containing samples collected in Lake Baikal during wildfires in the adjacent areas. The set of studied samples included the following: (i) water from the upper layer (5 m); (ii) water from the surface microlayer; (iii) water from the lake tributaries; (iv) water from deep layers (400 m); and (v) aerosol from the near-water layer. Ten PAHs were detected in the water samples: naphthalene, 1-methylnaphthalene, 2-methylnaphthalene acenaphthylene, acenaphthene, fluorene, phenanthrene, fluoranthene, pyrene, and chrysene. The total PAH concentrations (ƩPAHs) were detected in a wide range from 9.3 to 160 ng/L, characterizing by seasonal, intersessional, and spatial variability. In September 2016, the ƩPAH concentration in the southern basin of the lake reached 610 ng/L in the upper water layer due to an increase in fluorene, phenanthrene, fluoranthene, and pyrene in the composition of the PAHs. In June 2019, ƩPAHs in the water from the northern basin of the lake reached 290 ng/L, with the naphthalene and phenanthrene concentrations up to 170 ng/L and 92 ng/L, respectively. The calculation of back trajectories of the atmospheric transport near Lake Baikal, satellite images, and ƩPAH concentrations in the surface water microlayer of 150 to 960 ng/L confirm the impact of wildfires on Lake Baikal, with which the seasonal increase in the ƩPAH concentrations was associated in 2016 and 2019. The toxicity of PAHs detected in the water of the lake in extreme situations was characterized by the total value of the toxic equivalent for PAHs ranging from 0.17 to 0.22 ng/L, and a possible ecological risk of the impact on biota was assessed as moderate.