In this paper we present CFD simulations to model enzymatic reactions in microfluidic flow-through chambers. The chambers are filled with magnetic nanoparticles (MNPs). For the modeling we used the open source software OpenFOAM. The simulation settings are based on previous measurement results. The fluid flow, the effects of the magnetic nanoparticles and the enzymesubstrate reaction are being examined. Recently we designed new enhanced chamber geometries, in which the reaction simulations are also performed. The flow and the reaction are investigated at different temperatures.