To cool down the stack system in polymer electrolyte fuel cells (PEFCs), a coolant is needed that must be electrically nonconductive. In the specialized coolant that is modeled by us, charged nanoparticles are added into the flow to neutralize the ion contamination that otherwise gradually degrades the coolant until shunt currents become significant. A computational fluid dynamics (CFD) physicochemical model of the multiphase coolant flow with charged nanoparticles has been formulated and coded using COMSOL Multiphysics and MEMS. Electrochemistry, fluid mechanics, steric stabilization, and heat transfer are coupled in this model. For nanoparticles in the fluid, electrokinetic force, electrical double layer (EDL) force, hydrodynamic force, and buoyancy force have been taken into account for the prediction of the electrodeposition rate onto channel walls. The overall goal of the model is to provide a fundamental first principles-based design tool for a specialized coolant to enable operations in a fuel cell stack for 2−3 years without the need for frequent replacement or filtering of the coolant.