This paper describes a combined investigation of the salivary and MUC5B films structure and topography in conditions similar to those found in the oral cavity in terms of ionic strength, pH, and protein concentration. AFM and ellipsometry were successfully used to give a detailed picture of the film structure and topography both on hydrophilic and on hydrophobic substrata. Regardless of the substrata, the salivary film can be described as having a two sublayer structure in which an inner dense layer is decorated by large aggregates. However, the shape and height of these larger aggregates largely depend on the type of substrata used. Additionally, we show that the adsorption of MUC5B is controlled by the type of substrata and the MUC5B film topography is similar to that of the larger aggregates present in the salivary films, especially on hydrophobic substrates. Therefore, we conclude that MUC5B is a major component in the salivary film when formed on hydrophobic substrates. Furthermore, we studied how resistant the salivary and MUC5B films are against elutability by buffer rinsing and addition of SDS solution. We conclude that the adsorbed proteins contain fractions with varying binding strengths to the two types of surfaces. Specifically, we have shown that the large MUC5B biomacromolecules on the hydrophobic substrates are especially resistant to both elution with buffer solution and SDS. Therefore, these large mucins can be responsible for the increased resistance of HWS films on hydrophobic substrates and can protect the intraoral surfaces against surface-active components present in oral health care products.