Bio-inspired polydopamine coatings offer vast possibilities for surface modification of materials. The thickness of such nanometric coatings is usually estimated based on ellipsometry measurements. However, the complex light-absorbing nature of polydopamine is often overlooked when analyzing such data, which can result in inaccurate estimations of the coating thickness as well as the optical properties. In this study, we prepared and characterized three polydopamine coatings where the film thickness and surface roughness are systematically varied. For each case, we developed suitable optical models and showed how an inappropriate optical model can provide inaccurate estimates of the coating properties. AFM height profiles were obtained from scratched areas of each sample to verify the thickness values estimated by ellipsometry. The results confirm that polydopamine coatings, depending on the oxidation conditions, can possess different structural and optical properties, and thus require unique optical models for the ellipsometry analysis.