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Soils in nature are open non-equilibrium systems, which have a variable composition and structure. The effective value of their thermo-physical properties can change with time under the influence of changing environmental factors. Usually, thermo-physical properties of soils measured in situ differ from the estimates obtained in the laboratory. Presented here is a method of monitoring the temperature and heat flow to obtain data on the dynamics of effective thermal conductivity and effective heat capacity of soils in natural conditions. The use of both temperature and heat flow allows the calculation of thermo-physical coefficients using simple models that do not require a large number of constraints. Effective heat capacity of the soil was calculated by the equation of thermal balance of the soil layer. The heat conduction equation was used to calculate the effective thermal conductivity of the soil. The observed changes in effective rates of thermal conductivity and heat capacity of soils because the soil heat transfer with boundary environments occurs in non-equilibrium conditions. It is complicated phase transitions during freezing and thawing, evaporation and condensation, convection, mobile phases, heat effects of chemical reactions, interfacial interactions, biochemical transformations. In addition, temperature sensors and heat flux as a foreign body distort the temperature field in the soil and serve as barriers to convective heat and mass transfer. It should be supplemented the monitoring complex by measurements of moisture content, potential moisture and other indicators that characterize the dynamics of soil properties under natural conditions for adequate interpretation of the observed dynamics.