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A theoretical description of the convection-diffusion process in a homogeneous system enabling estimation of diffusion coefficients employing commercially available Y-junction microchannel is presented. A detailed numerical analysis based on finite volumes and finite differences, namely the explicit, implicit and Crank-Nicolson method, was performed and analyzed on the same domain in order to verify the proposed models. All numerical approaches provided stable solutions with certain numerical variations depending on the number of iterations defined by the mesh density. In addition, the method was validated with measurements of diffusion coefficients of some selected components in the short Y-junction microchannel. Benefits and possible pitfalls of this estimation method are discussed.