Solar cell degradation can occur through many pathways and at the different stages of the fabrication process, notably because of the water condensation. In the case of Cu(In,Ga)Se2 (CIGS) solar cells, the impact of water ingress on Mo back contact can be substantial for not only the film itself but also the device performance and reliability. Microstructural modification, change in film morphology, loss in reflectance, and increased resistivity because of the moisture ingress were observed via X-ray diffraction, transmission electron microscopy, spectroscopic ellipsometry, and four-point probe measurements, respectively. Secondary ion mass spectrometry measurements revealed drastic changes in the alkali (Na, K) profiles in both the CIGS and Mo layers, likely because of the modification of their diffusion coefficient through Mo. This, in turn, negatively impacts the solar cell efficiency by decreasing both fill factor and open-circuit voltage. Additional experiments, modifying the substrate and utilizing a NaF postdeposition treatment, highlight the mechanisms of degradation as being due to both a modification of the Mo/CIGS interface and the lack of alkali diffusion after water ingress.