Multi-cell niobium cavities often obtain the highest performance levels after having been subjected to an electropolishing (EP) process. The horizontal EP process first developed at KEK/Nomura Plating for TRISTAN cavities is being applied to TESLA-style cavities and other structures for the XFEL and ILC R&D. Jefferson Lab is presently carrying this activity in the US. Because the local electropolishing current density is highly temperature dependent, we have created using CFDesign a full-scale hydrodynamic model which simulates the various thermal conditions present during 9-cell cavity electropolishing. The results of these simulations are compared with exterior surface temperature data gathered during ILC cavity EP at JLab. Having benchmarked the simulation, we explore the affect of altered boundary conditions in order to evaluate potentially beneficial modifications to the current standard process.