Film formation of waterborne two-component polyurethanes is exceedingly complex due to the heterogeneous nature along with simultaneous progression of several parallel physicochemical processes which include water evaporation, cross-linking reactions, phase separation, and droplet coalescence, to name a few. While internal reflection infrared imaging (IRIRI) spectroscopy clearly facilitates analysis of chemical changes resulting from film formation, the complexity of processes leading to formation of specific surface/interfacial entities is a major experimental challenge. For this reason, we combined a spectrum of surface/interfacial analytical approaches including IRIRI, atomic force microscopy, and attenuated total reflectance Fourier transform infrared spectroscopy with Monte Carlo computer simulations to advance the limited knowledge of how temperature, stoichiometry, concentration levels, and reactivities of individual components affect the development of surface morphologies and compositional gradients across the film thickness. These studies show that in heterogeneous systems having both hydrophobic and hydrophilic components stratification of individual components to the film-air (F-A) interface is ultimately responsible for formation of rough surface topographies. These studies show that simultaneous stratification of hydrophobic components along with water evaporation to the F-A interface results in metastable interfacial layers, leading to surface dewetting. Subsequently, surface roughness is enhanced by higher concentrations of water in the cross-linking film.