Solutions of anolyte and catholyte obtained during diaphragm electrolysis as disinfectants or biostimulants are widely used not only in industry, but also in agriculture. One of the advantages of these solutions in comparison with traditional means is their environmental friendliness. Despite this, the mass application of these solutions in crop production, animal husbandry and other branches of agriculture is still difficult due to the lack of reliable flow-through installations for their production. This is primarily due to the low operational life of such installations. Modeling the processes occurring in diaphragm electrolyzers would simplify the process of their implementation in agriculture by improving their design. The conducted literature search showed the absence of mathematical models that would take into account the thermal, hydrodynamic and electrochemical processes occurring in flow-through diaphragm electrolyzers. The article deals with the simulation of these processes using the Comsol Multiphysics software. As a result of the simulation, images of the water pH in anode and cathode chambers of the electrolyzer, as well as temperature fields, were obtained and analyzed. It is determined that there is a section, after which the pH of the anolyte and the catholyte does not change significantly, what reduces the weight and size parameters of the installation in the channels of the flow-through diaphragm electrolyzer. A comparison of obtained theoretical and experimental data showed good convergence, which indicates the adequacy of the obtained mathematical model of physical and chemical processes in a flow-through diaphragm cell and the possibility of its further use for improving these installations in agriculture.