A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods; however, such a fundamental approach is perhaps critical for the realization of enhanced performance in traditional desalination and related treatments, and in the development of novel water treatment technologies. Specifically, we examine in this article the molecular-scale processes that affect water and ion selectivity at the nanopore scale as inspired by nature, the behavior of a model polysaccharide as a biofilm, and the use of cluster-surfactant flocculants in viral sequestration.