Mucus is a complex hydrogel biomaterial whose composition is regulated meticulously to ensure that its important function as a selective barrier is maintained. As part of this function, mucus regulates the uptake of molecules from the gastrointestinal lumen into the body. Yet, those hydrogels are continuously challenged with environmental pollutants such as black carbon nanoparticles (NPs), and there is growing evidence that these contaminants can compromise the functionality of mucus. Here, we assess the impact of black carbon NP contaminations on the selective permeability properties of mucin hydrogels. For this purpose, we identified two physiologically relevant black carbon concentrations and used those NP concentrations to perform molecular penetration studies with pristine and contaminated mucin hydrogels. We found that the presence of black carbon NPs enhances both the partitioning of anionic molecules into mucin hydrogels and the translocation of cationic molecules across those barriers. Moreover, we found that this permeability modulating effect is asymmetric with respect to charge; i.e., the penetration and translocation behavior of cationic molecules is affected more strongly than that of anionic ones. To rationalize those findings, we propose that black carbon NPs are well integrated into the mucin glycoprotein network, thus masking more anionic binding sites on mucins than creating cationic ones. Our results underscore the high value of suitable in vitro models when trying to decipher the nanoscopic effects by which physiologically relevant contaminants can influence molecular transport phenomena across mucosal barriers.