The vertical distribution of microplastics in Lake Ladoga was studied under conditions of density stratification with the presence of a thermocline and under homothermal conditions. Using a pump filtration device, water samples were taken at different water layers (0–70 m) under different hydrological conditions and a comparative analysis of the concentrations of microplastic particles with a size of 60–5000 μm was carried out. Microplastic particles were analyzed using both optical microscopy and Raman spectroscopy methods. Based on the obtained data, it was concluded that under conditions of density stratification, the concentrations of microplastic particles in the thermocline and above it are increased in comparison with the underlying layers (50 ± 40.2 and 15.9 ± 13 particles/m3, respectively). Under homothermal conditions, the vertical distribution of microplastics in the surface layer and in water column is more uniform (17.3 ± 17.8 and 12.7 ± 15.6 particles/m3, respectively).