Waterborne polyurethane synthesis was performed using a prepolymer method based on poly(tetramethylene ether glycol) and isophorone diisocyanate. Polydimethylsiloxane and/or perfluorinated polyether was then introduced to the system as soft segments to prepare modified waterborne polyurethanes. Fourier transform infrared spectroscopy confirmed that silicone and fluorine were successfully incorporated into the chain of the WPU polymer. The surface properties of the resultant WPU polymers were characterized by X-ray photoelectron spectroscopy (XPS) and contact angle (CA) measurements. An improved CA, a decrease in the surface free energy, and a remarkable enrichment of silicon and fluorine at the film-air interface confirmed the surface mobility of the silicon and fluorine moieties, which results from their low surface energy. However, the XPS data indicated that the ability of these moieties to migrate was mutually inhibited when they were both present in the polymer backbone. In addition, the mechanical properties of the polymer were improved significantly when PDMS or E10-H was introduced into the backbone. A favorable synergistic effect was observed when both silicon and fluorine moieties were included in the polyurethane chain, yielding WPU films with the highest tensile strength (27 MPa). Finally, the extent of variable phase separation, caused by mobility and incompatibility between the silicone and fluorine moieties and the WPU segment, was observed in the WPU film matrix by scanning electron microscopy.