We studied silica suspensions with chitosan and biodegradable synthetic surfactant lauroyl ethyl arginate (LAE). Hydrophilic and negatively charged silica nanoparticles were neutralised due to the coating with chitosan. That presence of LAE led to the partial hydrophobisation of their surface, which favoured their attachment to the surface of a thin foam film. It was found that the presence of small and medium-sized (6–9 nm) hydrophobic particles in the interfacial layer of lamella foam film inhibited the coalescence and coarsening processes, which prolonged the life of the foam. Furthermore, hydrophobising of 30 nm particles allowed the formation of large aggregates precipitating from the mixture under steady-state conditions. These aggregates, however, under the conditions of the dynamic froth flotation process in the foam column, were floated into the foam layer. As a result, they were trapped in the foam film and Plateau borders, effectively preventing liquid leakage out of the foam. These results demonstrate the efficiency of using chitosan-LAE mixtures to remove silica nanoparticles from aqueous phase by foaming and flotation.