It has been shown that using nanofluids as heat carrier fluids enhances the conductive and convective heat transfer of geothermal heat exchangers. In this paper, we study the stability of nanofluids in a geothermal exchanger by numerically simulating nanoparticle sedimentation during a shut-down process. The nanofluid suspension is modeled as a non-linear complex fluid; the nanoparticle migration is modeled by a particle flux model, which includes the effects of Brownian motion, gravity, turbulent eddy diffusivity, etc. The numerical results indicate that when the fluid is static, the nanoparticle accumulation appears to be near the bottom borehole after many hours of sedimentation. The accumulated particles can be removed by the fluid flow at a relatively high velocity. These observations indicate good suspension stability of the nanofluids, ensuring the operational reliability of the heat exchanger. The numerical results also indicate that a pulsed flow and optimized geometry of the bottom borehole can potentially improve the suspension stability of the nanofluids further.