Microreactors are miniaturized reaction systems with caracteristic dimensions of microchannels of less than 500 μm. In comparison to the conventional reactors, microreactors have a significantly greater specific surface to volume ratio, which is the reason for more intensive mass and heat transfer. Smaller amount of chemicals required for carrying out the process and improved control of work conditions cause reduction of waste. Furthermore, positive influence on environment have deep eutectic solvents, also recognized as green solvents, due to properties such as biodegradability, reduced toxicity and simplicity of preparation and purification. In this thesis the analysis of the diffusion of two-phase water-eutectic solvent diffusion was performed in two microreactors with the same configuration, but different microchannel width (250 μm, 500 μm) and volume (4,13 μL, 8,30 μL). Deep eutectic solvents choline chloride:glycerol and choline chloride:glucose with diferent water content (30 %, 50 %, 80 %) were synthesized and their density, viscosity and surface tension were determined. Dyed water and the deep eutectic solvent were separately introduced into the microreactor at different total flow rates (Q = 1 – 200 μL/min), i.e. different retention times. Dimensionless numbers (Reynolds and Capillary number) were determined for the flow profile analysis. Relative concentration of the dye was experimentally measured and compared to the mathematical model solved by a simple numerical approximation for solving system of partial differential equation describing the diffusion process in the two-phase water-deep eutectic solvent system.