To stabilize and transport them through complex systems, nanoparticles are often encapsulated in polymeric nanocarriers, which are tailored to specific environments. For example, a hydrophilic polymer capsule maintains the circulation and stability of nanoparticles in aqueous environments. A more highly designed nanocarrier might have a hydrophobic core and a hydrophilic shell to allow the transport of hydrophobic nanoparticles and pharmaceuticals through physiological media. Polydimethylsiloxane, PDMS, is a hydrophobic material in a liquid-like state at room temperature. The preparation of stable, aqueous dispersions of PDMS droplets in water is problematic due to the intense mismatch in surface energies between PDMS and water. The present work describes the encapsulation of hydrophobic metal and metal oxide nanoparticles within PDMS nanodroplets using flash nanoprecipitation. The PDMS is terminated by amino groups, and the nanodroplet is capped with a layer of poly(styrenesulfonate), forming a glassy outer shell. The hydrophobic nanoparticles nucleate PDMS droplet formation, decreasing the droplet size. The resulting nanocomposite nanodroplets are stable in aqueous salt solutions without the use of surfactants. The hierarchical structuring, elucidated with small-angle X-ray scattering, offers a new platform for the isolation and transport of hydrophobic molecules and nanoparticles through aqueous systems.