The effect of different variants of compiling integrated samples for biochemical oxygen demand (BOD) kinetics was studied in long-term experiments (up to 84–126 days) with water samples taken from the central deep-water region of Lake Onego. It was a series of 32 experiments carried out simultaneously at 10 and 20 °С in different seasons of 2012–2017. Five sampling variants were employed with different horizon combinations: near surface, near bottom, from different depths in the water column, from the photic and profundal layers. Two experiments were performed with winter water, three with summer water, four with autumn water, and seven experiments with spring water. The most representative sample for studying BOD in long-term experiments is an sample composed of water from different horizons of the photic layer (0.5–13 m). For each variant of integrated sample composition, BOD development in the experiments was modeled by a corresponding kinetic equation whose parameters represented the oxidation characteristics of components of the organic matter present in the water and transformed in the long-term BOD experiment. The resultant kinetic parameters of BOD were analyzed in relation to the factors determining the final oxidation of the organic matter components. The patterns in which the type of BOD development is formed depend on the integrated water sample collection/compilation conditions and are characterized by the average values of the organic matter contained in the water, estimated either analytically or from empirical equations, as well as by the temperature of exposure of water samples in the experiment. Synthesis of the resultant information showed that the values of BOD kinetic parameters were generally lower in spring water taken from the central part of Lake Onego as compared with other seasons, since the oxidation potential of organic matter components in spring water is higher.