Heat transfer of aqueous flows was studied in a Y-shaped microreactor at different flow rates. In order to analyze the experimental data and to forecast the microreactor performance, a three-dimensional mathematical model with convection and conduction was developed, considering the velocity profile for laminar flow at steady state. The dependence of temperature on the thermophysical properties of water was implemented into the mathematical model. The microreactor investigated consists of a rectangular microchannel, which is divided into two inlet channels, a central channel, and two outlet channels. The average temperatures of water outflows were monitored. Very good agreement with the model calculations and the experimental data was achieved without any fitting procedure. In addition, the transition from laminar to turbulent flow was studied for different microchannel geometries, and the results showed that the channel aspect ratio and the angle of merging of two inlet channels substantially influence the critical Reynolds number.