Electrochromic thin films must be highly stable against heat and moisture for their application to devices operating in air atmosphere. In this study, we discuss the degradation of the surface morphology of sputtered WO3 thin films in heated water. When the water temperature and soaking times increase, the flat surface of film undergoes a pronounced transition and becomes rough causing partial etching off the film. Although the surface area available for ion intercalation increases by etching, the electrochromic performance of films degrades. We propose stacking a passivation layer of Nb2O5 to prevent the etching off the WO3 thin films and changes in their surface morphology. The surface morphology of the bilayer thin films soaked in water at 70 °C for 30 and 180 s does not change noticeably when the thicknesses of the Nb2O5 layers are 25 and 100 nm, respectively. Both the thin films exhibit transmittance modulations and coloration efficiencies comparable to those of the WO3 thin film without etching, suggesting effective passivation. Moreover, the stacks are stable during cyclic tests up to 700 cycles in an H2SO4 solution. In contrast, the soaked WO3 thin films lose their electrochromic switching capability after the 35th cycle. In conclusion, Nb2O5 passivation of WO3 thin films can effectively prevent their degradation under hot and moist conditions.