The paper presents the physical methods of investigations of natural environment and food products applied in agrophysics. Experimental methods of investigations of hydro- and thermophysical processes in the soil-plant-atmosphere system were described. Modelling of the processes of mass and energy transfer in the soil-plant-atmosphere system with use of the principle of mass and energy conservation and thermodynamical principles were discussed. Special attention was payed to direct and indirect methods of measurements of evapotranspiration. Problems of agrophysical metrology were discussed basing on an example of application of teledetection for remote measurement of radiational temperature of plants for elaboration of measuring methods of water conditions for systems of hydrotechnical management and redistrubution of water in the rural areas. Application of physical methods of investigations for decreasing qualitative and quantitative losses of plant materials resulting from incorrect evaluation of impact of applied technologies (harvest and processing) was indicated. Modern methods of quality evaluation and sorting of agricultural products based on the detection of various physical properties which correlate well with certain quality factors of the products were discussed. Modelling of the rheological properties which allow for quick evaluation of maturity of fruits and vegetables, influence of storage conditions and the resistance to mechanical loads were considered. Problems of storage of cereal grains and oilseeds were discussed. The most important technological parameters (time, temperature, pressure) and seed parameters (moisture, fine particle content, maturity stage) influencing quality of rape seeds during storage were indicated. Physical properties of granular materials of biological origin influencing storage, handling and processing were discussed.