The motion of small slightly deformed bubbles rising in stagnant liquids was numerically simulated in a fully three-dimensional domain using the commercial CFD (Computational Fluid Dynamics) solver COMSOL Multiphysics. The interface was tracked by the built-in conservative Level set method on a fixed numerical grid. The purpose of this work was to validate the ability of the solver to calculate the single bubble motion in liquids, which differ in surface tension, dynamic viscosity, and density. Experimental data for three liquids and various initial bubble diameters (1–1.6mm) together with the recommended theoretical models were used for validation. Using a 3D domain, very good agreement was obtained both in bubble shape deformations and values of bubble terminal velocity. The best results were achieved for a liquid with low surface tension and low viscosity (1-propanol). In the case of high surface tension and low viscosity liquid (water) the solver underestimates bubble deformation and the bubble velocity. In case of glycerol (high surface tension and viscosity), the low bubble deformation is correctly calculated, but the velocity is underestimated.