The advantages of miniaturized systems and the laminar flow regime that is present in microfluidic channels have opened a new range of applications in which the use of multiple streams with different reagents is exploited. However, further development of these microdevices needs deeper understanding on the phenomena involved in order to efficiently design such microsystems. In this work, we report the analysis of the solute mass transport performance in Y-Y-shaped microchannels as a function of the coupled influence of both the flow patterns and mass transport kinetics. With this objective, the influence of the following operation variables has been analyzed, the ratio between the residence and diffusion times (gamma) and the volumetric ratio between the fluid phases (alpha), that was determined for three different geometric configurations. The performance of the devices was presented as the solute separation factor in the donor fluid and the concentration factor in the receiving phase. Results showed that the ratio alpha greatly impacts the solute concentration value reported in both phases for the same gamma value, which in turn influences the solute mass flow at the channel outlets. Both the flow patterns and the concentration gradients developed inside the systems were numerically studied by using Computational Fluid Dynamics (CFD) techniques and experimentally analyzed by fluorescence microscopy with fluorescein employed as model solute. This study represents a thorough analysis of the phenomena that determine the performance of the separation of solutes between homogeneous flowing fluids in microdevices where the fluid dynamics are coupled with mass transfer phenomena and facilitates its extension to the general case where separation is enhanced by chemical reactions.