The microstructure of a polymer coating plays an important role in the water uptake behavior. This paper aims to correlate the molecular mobility and the water–polymer interactions with the microstructures of a highly cross-linked PU system. GARfield NMR imaging was used to monitor in situ the water uptake of the PU coating at different temperatures. The results of continuum T2 fitting show that at temperatures below the enthalpy relaxation temperature (65 °C) the PU coating uptakes water, whereas the polymer matrix is not plasticized by the presence of water. At higher temperatures, however, the polymer matrix is significantly mobilized by the presence of water molecules as indicated by the appearance of the longer T2 component. The water content in the PU coating is monitored by GARfield NMR at different temperatures. The results show that the water content decreases in two steps as the temperature decreases from 85 °C to the room temperature. This result is explained in combination with the molecular relaxation phenomenon probed by the DSC. A microstructure model was formulated based on the experimental results.