Combining organic and inorganic components at a nanoscale is an effective way to obtain high performance coating materials with excellent chemical and physical properties. This review focuses on recent approaches to prepare hybrid nanostructured waterborne coating materials combining the mechanical properties and versatility of silica as the inorganic filler, with the flexural properties and ease of processing of the polymer matrix. We cover silica-polymer coupling agents used to link the organic and inorganic components, the formation of hybrid films from these silica-polymer nanostructures, and their different applications. These hybrid nanostructures can be used to prepare high performance functional coatings with different properties from optical transparency, to resistance to temperature, hydrophobicity, anti-corrosion, resistance to scratch, and antimicrobial activity.