Long-term BOD experiments (up to 84–126 days) were conducted and the concentrations of organic matter compounds were determined in different seasons of 2013–2017 with water taken from different parts of Lake Onego: Pukhtа, Kondopoga, Petrozavodsk Bays, as well as the estuarine zone of the River Shuya and the area around Ivanovskie Islands. Water samples were taken either from the surface horizon (0.5 or 1 m) or fromdifferent water column horizons (from the surface to the bottom). In total, 48 experiments were held: 16 experiments were performed simultaneously for 20 and 10 oC, and eight – for 10 and 2 oC, respectively. The development of BOD in all the experiments was modeled by various types of kinetic equations with parameters that also reflect season-averaged characteristics of BOD kinetics in the first, second and linear stages. The average spring and summer values of water BOD parameters in the above-listed regions of Lake Onego were higher than the values in water from the Central region of the lake. It was shown that O2 consumption in the lake’s peripheral water areas at the first stage of oxidation of labile organic components and in the linear stage of oxidation of conventionally “stable” organic fractions in different seasons was, respectively, 2.5–4.2 and 2 times higher compared to the Central part of the lake. This is additional evidence of the high water quality retained in the Central region. Strong correlation was found between different organic matter components and BOD kinetic parameters (R2 = 0.60–1.00).