Abstract To investigate the rinsing process in single-wafer spin cleaning, we simulated a three-dimensional unsteady replacement process in which pure water from a nozzle replaced a chemical solution on a rotating disk. The simulation used a two-phase flow solver provided by OpenFOAM combined with our modified approach for advective–diffusive transport of the chemical concentration in the liquid phase. We analyzed the effect of the nozzle position by performing computations with water supplied on- and off-axes. In the axisymmetric configuration, the solution displacement near the disk edge was challenging; in the nonaxisymmetric configuration, it was difficult around the disk center. Axisymmetric two-dimensional computations were also conducted to examine the replacement speed. The replacement of trace concentrations was strongly dependent on shear flow-driven concentration gradients, which facilitate molecular diffusion. The replacement rate was accelerated by the steepening of shear flow due to jet stagnation pressure and centrifugal forces from the disk rotation.